4-161237218-T-C

Variant names:

• chr4-161237218-T-C
• rs10517739
• ENST00000816576.1:n.314+5722A>G

Variant summary

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

The ENST00000816576.1(ENSG00000306264):​n.314+5722A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,660 control chromosomes in the GnomAD database, including 7,613 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 0.31 (7613 hom., cov: 32)
• Consequence: ENSG00000306264 ENST00000816576.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494
• Publications: 5 publications found

Genes affected

ENSG00000306264 (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 = 0.397 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816576.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306264	ENST00000816576.1		n.314+5722A>G		intron	N/A
	ENSG00000306264	ENST00000816577.1		n.313+5722A>G		intron	N/A
	ENSG00000306264	ENST00000816578.1		n.339+5722A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47296 AN: 151542 Hom.: 7599 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.312 AC: 47345 AN: 151660 Hom.: 7613 Cov.: 32 AF XY: 0.305 AC XY: 22628 AN XY: 74142

African (AFR) AF: 0.402 AC: 16661 AN: 41440

American (AMR) AF: 0.301 AC: 4579 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1122 AN: 3464

East Asian (EAS) AF: 0.303 AC: 1561 AN: 5156

South Asian (SAS) AF: 0.186 AC: 893 AN: 4812

European-Finnish (FIN) AF: 0.199 AC: 2108 AN: 10588

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19424 AN: 67686

Other (OTH) AF: 0.311 AC: 653 AN: 2102

Alfa AF: 0.293 Hom.: 8089

Bravo AF: 0.322

Asia WGS AF: 0.228 AC: 790 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.83
PhyloP100		-0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10517739;

hg19: chr4-162158370;