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:58801):

LOC105377265 (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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766642.1. 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
	ENSG00000299813	ENST00000766642.1		n.52-3162T>G		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs7435274;

hg19: chr4-69915999;