dbSNP rs1128723: MFSD6:c.*1763A>G (chr2-190501981-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017694.4(MFSD6):c.*1763A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,616 control chromosomes in the GnomAD database, including 2,385 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2385 hom., cov: 32)

Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

MFSD6
NM_017694.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540

Publications

16 publications found

Variant links:

Genes affected

MFSD6 (HGNC:24711): (major facilitator superfamily domain containing 6) Predicted to enable MHC class I protein binding activity and MHC class I receptor activity. Predicted to be involved in antigen processing and presentation of exogenous peptide antigen via MHC class I. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

MFSD6 links:

NEMP2 (HGNC:33700): (nuclear envelope integral membrane protein 2) Predicted to be located in nuclear inner membrane. Predicted to be integral component of membrane. Predicted to be active in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

NEMP2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MFSD6	NM_017694.4 link	c.*1763A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000392328.6	NP_060164.3	Q6ZSS7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MFSD6	ENST00000392328.6 link	c.*1763A>G	3_prime_UTR_variant	Exon 8 of 8	2	NM_017694.4	ENSP00000376141.1	Q6ZSS7
MFSD6	ENST00000281416.11 link	c.*1763A>G	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000281416.7	Q6ZSS7
MFSD6	ENST00000434582.5 link	c.*1956A>G	3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000397276.1	H7C0X2
MFSD6	ENST00000412482.1 link	n.*58+1705A>G	intron_variant	Intron 2 of 3	3		ENSP00000404511.1	H7C284

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

26045

AN:

152068

Hom.:

2383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.0859

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.175

Gnomad OTH

AF:

0.165

GnomAD4 exome

AF:

0.0829

AC:

AN:

434

Hom.:

Cov.:

AF XY:

0.0802

AC XY:

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.0845

AC:

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.171

AC:

26063

AN:

152182

Hom.:

2385

Cov.:

AF XY:

0.167

AC XY:

12459

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.185

AC:

7692

AN:

41526

American (AMR)

AF:

0.133

AC:

2035

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.119

AC:

412

AN:

3470

East Asian (EAS)

AF:

0.305

AC:

1575

AN:

5166

South Asian (SAS)

AF:

0.191

AC:

918

AN:

4816

European-Finnish (FIN)

AF:

0.0859

AC:

910

AN:

10596

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.175

AC:

11914

AN:

67996

Other (OTH)

AF:

0.169

AC:

358

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1115

2229

3344

4458

5573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.177

Hom.:

5808

Bravo

AF:

0.176

Asia WGS

AF:

0.242

AC:

841

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.9

(source)

DANN

Benign

0.73

PhyloP100

-0.054

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs1128723

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over