rs7435274

Variant names:

• chr4-69050281-A-C
• rs7435274
• ENST00000766642.1:n.52-3162T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-69050281-A-C
• chr4-69050281-A-T

Variant summary

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

The ENST00000766642.1(ENSG00000299813):​n.52-3162T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,992 control chromosomes in the GnomAD database, including 17,583 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 0.46 (17583 hom., cov: 32)
• Consequence: ENSG00000299813 ENST00000766642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.19
• Publications: 3 publications found

Genes affected

ENSG00000299813 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377265	XR_001741714.2	n.3048-145T>G		intron_variant	Intron 2 of 4
LOC105377265	XR_938851.2	n.316-145T>G		intron_variant	Intron 1 of 3
LOC105377265	XR_938852.2	n.316-253T>G		intron_variant	Intron 1 of 3
LOC105377265	XR_938854.2	n.298-145T>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299813	ENST00000766642.1	n.52-3162T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69966 AN: 151872 Hom.: 17558 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.461 AC: 70035 AN: 151992 Hom.: 17583 Cov.: 32 AF XY: 0.461 AC XY: 34230 AN XY: 74288

African (AFR) AF: 0.658 AC: 27274 AN: 41462

American (AMR) AF: 0.425 AC: 6493 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1776 AN: 3464

East Asian (EAS) AF: 0.575 AC: 2979 AN: 5178

South Asian (SAS) AF: 0.429 AC: 2062 AN: 4806

European-Finnish (FIN) AF: 0.357 AC: 3764 AN: 10552

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24247 AN: 67946

Other (OTH) AF: 0.467 AC: 984 AN: 2106

Alfa AF: 0.249 Hom.: 618

Bravo AF: 0.475

Asia WGS AF: 0.479 AC: 1661 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.27
DANN	Benign	0.16
PhyloP100		-4.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7435274; hg19: chr4-69915999;