rs1128723

Variant summary

Our verdict is Benign. Variant got -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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0540
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
MFSD6NM_017694.4 linkuse as main transcriptc.*1763A>G 3_prime_UTR_variant 8/8 ENST00000392328.6 NP_060164.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MFSD6ENST00000392328.6 linkuse as main transcriptc.*1763A>G 3_prime_UTR_variant 8/82 NM_017694.4 ENSP00000376141 P1
MFSD6ENST00000281416.11 linkuse as main transcriptc.*1763A>G 3_prime_UTR_variant 6/61 ENSP00000281416 P1
MFSD6ENST00000434582.5 linkuse as main transcriptc.*1956A>G 3_prime_UTR_variant 7/75 ENSP00000397276
MFSD6ENST00000412482.1 linkuse as main transcriptc.*58+1705A>G intron_variant, NMD_transcript_variant 3 ENSP00000404511

Frequencies

GnomAD3 genomes
AF:
0.171
AC:
26045
AN:
152068
Hom.:
2383
Cov.:
32
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:
36
AN:
434
Hom.:
0
Cov.:
0
AF XY:
0.0802
AC XY:
21
AN XY:
262
show subpopulations
Gnomad4 FIN exome
AF:
0.0845
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.171
AC:
26063
AN:
152182
Hom.:
2385
Cov.:
32
AF XY:
0.167
AC XY:
12459
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.185
Gnomad4 AMR
AF:
0.133
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.305
Gnomad4 SAS
AF:
0.191
Gnomad4 FIN
AF:
0.0859
Gnomad4 NFE
AF:
0.175
Gnomad4 OTH
AF:
0.169
Alfa
AF:
0.177
Hom.:
4003
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
DANN
Benign
0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1128723; hg19: chr2-191366707; API