rs7674640

Variant names:

• chr4-102619623-C-T
• rs7674640
• ENST00000802886.1:n.129+1080G>A

Variant summary

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

The ENST00000802886.1(ENSG00000304360):​n.129+1080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.557 in 151,894 control chromosomes in the GnomAD database, including 24,080 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 0.56 (24080 hom., cov: 32)
• Consequence: ENSG00000304360 ENST00000802886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 33 publications found

Genes affected

ENSG00000304360 (HGNC:58861):

LOC105377347 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802886.1. 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
	ENSG00000304360	ENST00000802886.1		n.129+1080G>A		intron	N/A
	ENSG00000304360	ENST00000802887.1		n.130+1080G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84502 AN: 151776 Hom.: 24042 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.557 AC: 84585 AN: 151894 Hom.: 24080 Cov.: 32 AF XY: 0.555 AC XY: 41172 AN XY: 74220

African (AFR) AF: 0.676 AC: 28049 AN: 41462

American (AMR) AF: 0.569 AC: 8692 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1747 AN: 3460

East Asian (EAS) AF: 0.476 AC: 2454 AN: 5152

South Asian (SAS) AF: 0.493 AC: 2372 AN: 4812

European-Finnish (FIN) AF: 0.457 AC: 4811 AN: 10518

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34595 AN: 67912

Other (OTH) AF: 0.556 AC: 1170 AN: 2106

Alfa AF: 0.559 Hom.: 3616

Bravo AF: 0.570

Asia WGS AF: 0.510 AC: 1769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.10
DANN	Benign	0.17
PhyloP100		-1.7

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: rs7674640;

hg19: chr4-103540780;