3-34703260-T-C

Variant names:

• chr3-34703260-T-C
• rs2358503
• ENST00000721753.1:n.97-26649A>G

Variant summary

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

The ENST00000721753.1(ENSG00000294183):​n.97-26649A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,658 control chromosomes in the GnomAD database, including 12,124 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 0.39 (12124 hom., cov: 29)
• Consequence: ENSG00000294183 ENST00000721753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 0 publications found

Genes affected

ENSG00000294183 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000721753.1. 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
	ENSG00000294183	ENST00000721753.1		n.97-26649A>G		intron	N/A
	ENSG00000294183	ENST00000721754.1		n.96-2365A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58841 AN: 151540 Hom.: 12089 Cov.: 29

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.389 AC: 58935 AN: 151658 Hom.: 12124 Cov.: 29 AF XY: 0.399 AC XY: 29530 AN XY: 74082

African (AFR) AF: 0.460 AC: 18993 AN: 41306

American (AMR) AF: 0.440 AC: 6700 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 697 AN: 3466

East Asian (EAS) AF: 0.654 AC: 3363 AN: 5144

South Asian (SAS) AF: 0.495 AC: 2372 AN: 4792

European-Finnish (FIN) AF: 0.426 AC: 4485 AN: 10524

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21214 AN: 67896

Other (OTH) AF: 0.359 AC: 755 AN: 2102

Alfa AF: 0.344 Hom.: 5003

Bravo AF: 0.390

Asia WGS AF: 0.540 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-1.8

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: rs2358503;

hg19: chr3-34744752;