5-157718184-T-C

Variant names:

• chr5-157718184-T-C
• rs7731936
• ENST00000838702.1:n.176-2066A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000838702.1(ENSG00000309117):​n.176-2066A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,960 control chromosomes in the GnomAD database, including 17,565 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 0.48 (17565 hom., cov: 31)
• Consequence: ENSG00000309117 ENST00000838702.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 4 publications found

Genes affected

ENSG00000309117 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838702.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309117	ENST00000838702.1		n.176-2066A>G		intron	N/A
	ENSG00000309117	ENST00000838704.1		n.167-84A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72197 AN: 151842 Hom.: 17530 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.476 AC: 72291 AN: 151960 Hom.: 17565 Cov.: 31 AF XY: 0.478 AC XY: 35493 AN XY: 74284

African (AFR) AF: 0.562 AC: 23267 AN: 41410

American (AMR) AF: 0.400 AC: 6102 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1683 AN: 3466

East Asian (EAS) AF: 0.464 AC: 2397 AN: 5166

South Asian (SAS) AF: 0.495 AC: 2385 AN: 4820

European-Finnish (FIN) AF: 0.507 AC: 5344 AN: 10546

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29791 AN: 67980

Other (OTH) AF: 0.479 AC: 1009 AN: 2108

Alfa AF: 0.458 Hom.: 2731

Bravo AF: 0.469

Asia WGS AF: 0.476 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.48
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7731936; hg19: chr5-157145192;