chr2-190442682-G-T

Position:

• chr2-190442682-G-T

Variant summary

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

The NM_017694.4(MFSD6):​c.1532+5121G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,850 control chromosomes in the GnomAD database, including 9,175 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 0.33 (9175 hom., cov: 31)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: MFSD6 NM_017694.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD6	NM_017694.4	c.1532+5121G>T		intron_variant		ENST00000392328.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD6	ENST00000392328.6	c.1532+5121G>T		intron_variant		2	NM_017694.4	P1
MFSD6	ENST00000281416.11	c.1532+5121G>T		intron_variant		1		P1
MFSD6	ENST00000434582.5	c.138+5121G>T		intron_variant		5
MFSD6	ENST00000489793.1	n.107G>T		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50427 AN: 151722 Hom.: 9148 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.308

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.333 AC: 50498 AN: 151840 Hom.: 9175 Cov.: 31 AF XY: 0.343 AC XY: 25466 AN XY: 74198

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.308

Alfa AF: 0.269 Hom.: 7978

Bravo AF: 0.346

Asia WGS AF: 0.331 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.61

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: rs4129081; hg19: chr2-191307408;