4-157980512-G-A

Variant names:

• chr4-157980512-G-A
• rs4072169
• ENST00000660468.1:n.769+7194C>T

Variant summary

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

The ENST00000660468.1(ENSG00000287226):​n.769+7194C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,140 control chromosomes in the GnomAD database, including 5,516 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 0.24 (5516 hom., cov: 33)
• Consequence: ENSG00000287226 ENST00000660468.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 2 publications found

Genes affected

ENSG00000287226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660468.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287226	ENST00000660468.1		n.769+7194C>T		intron	N/A
	ENSG00000287226	ENST00000809819.1		n.346+7194C>T		intron	N/A
	ENSG00000287226	ENST00000809820.1		n.212+7194C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36208 AN: 152022 Hom.: 5498 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.238 AC: 36233 AN: 152140 Hom.: 5516 Cov.: 33 AF XY: 0.246 AC XY: 18306 AN XY: 74388

African (AFR) AF: 0.177 AC: 7354 AN: 41504

American (AMR) AF: 0.312 AC: 4769 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3468

East Asian (EAS) AF: 0.756 AC: 3918 AN: 5180

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4822

European-Finnish (FIN) AF: 0.187 AC: 1982 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14479 AN: 67984

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.224 Hom.: 1949

Bravo AF: 0.243

Asia WGS AF: 0.576 AC: 1998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.63
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4072169; hg19: chr4-158901664;