2-158866994-G-T

Variant names:

• chr2-158866994-G-T
• rs6757197
• ENST00000671005.1:n.1737+1663C>A

Variant summary

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

The ENST00000671005.1(ENSG00000286621):​n.1737+1663C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,894 control chromosomes in the GnomAD database, including 22,934 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 0.53 (22934 hom., cov: 32)
• Consequence: ENSG00000286621 ENST00000671005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

ENSG00000286621 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286621	ENST00000671005.1	n.1737+1663C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80752 AN: 151774 Hom.: 22902 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.539

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.532 AC: 80821 AN: 151894 Hom.: 22934 Cov.: 32 AF XY: 0.522 AC XY: 38787 AN XY: 74260

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.0646

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.552

Alfa AF: 0.582 Hom.: 32711

Bravo AF: 0.516

Asia WGS AF: 0.234 AC: 819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6757197; hg19: chr2-159723506;