rs6757698

chr2-190498770-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017694.4(MFSD6):c.2172+1051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,148 control chromosomes in the GnomAD database, including 5,052 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 0.23 (5052 hom., cov: 32)
• Consequence: MFSD6 NM_017694.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

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]

NEMP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD6	NM_017694.4	c.2172+1051T>C		intron_variant		ENST00000392328.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD6	ENST00000392328.6	c.2172+1051T>C		intron_variant		2	NM_017694.4	P1
MFSD6	ENST00000281416.11	c.2172+1051T>C		intron_variant		1		P1
MFSD6	ENST00000434582.5	c.778+1051T>C		intron_variant		5
MFSD6	ENST00000412482.1	c.71+1051T>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35306 AN: 152030 Hom.: 5050 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0774

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.232

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.232 AC: 35296 AN: 152148 Hom.: 5052 Cov.: 32 AF XY: 0.231 AC XY: 17191 AN XY: 74372

Gnomad4 AFR AF: 0.0867

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.0770

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.231

Alfa AF: 0.286 Hom.: 1410

Bravo AF: 0.207

Asia WGS AF: 0.255 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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

Other links and lift over

dbSNP: rs6757698; hg19: chr2-191363496;