4-6889728-T-G

Variant names:

• chr4-6889728-T-G
• rs11731274
• ENST00000779681.1:n.629+5115A>C

Variant summary

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

The ENST00000779681.1(ENSG00000301554):​n.629+5115A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,236 control chromosomes in the GnomAD database, including 2,560 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 0.16 (2560 hom., cov: 33)
• Consequence: ENSG00000301554 ENST00000779681.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 11 publications found

Genes affected

ENSG00000301554 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779681.1. 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
	ENSG00000301554	ENST00000779681.1		n.629+5115A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23952 AN: 152118 Hom.: 2559 Cov.: 33

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.157 AC: 23948 AN: 152236 Hom.: 2560 Cov.: 33 AF XY: 0.159 AC XY: 11833 AN XY: 74420

African (AFR) AF: 0.0589 AC: 2450 AN: 41574

American (AMR) AF: 0.195 AC: 2986 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2881 AN: 5166

South Asian (SAS) AF: 0.161 AC: 776 AN: 4830

European-Finnish (FIN) AF: 0.193 AC: 2049 AN: 10590

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11912 AN: 67986

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.152 Hom.: 1072

Bravo AF: 0.158

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.66
PhyloP100		-0.19

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: rs11731274;

hg19: chr4-6891455;