3-32223499-C-T

Variant names:

• chr3-32223499-C-T
• rs4376071
• ENST00000743257.1:n.266-8357G>A

Variant summary

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

The ENST00000743257.1(ENSG00000296868):​n.266-8357G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,948 control chromosomes in the GnomAD database, including 32,383 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 0.65 (32383 hom., cov: 31)
• Consequence: ENSG00000296868 ENST00000743257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601
• Publications: 5 publications found

Genes affected

ENSG00000296868 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296868	ENST00000743257.1	n.266-8357G>A		intron_variant	Intron 1 of 1
ENSG00000296868	ENST00000743258.1	n.196+6071G>A		intron_variant	Intron 1 of 2
ENSG00000296868	ENST00000743259.1	n.196+6071G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98060 AN: 151830 Hom.: 32386 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.646 AC: 98099 AN: 151948 Hom.: 32383 Cov.: 31 AF XY: 0.642 AC XY: 47703 AN XY: 74260

African (AFR) AF: 0.514 AC: 21285 AN: 41398

American (AMR) AF: 0.619 AC: 9459 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2145 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3589 AN: 5138

South Asian (SAS) AF: 0.613 AC: 2954 AN: 4816

European-Finnish (FIN) AF: 0.715 AC: 7552 AN: 10566

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48937 AN: 67974

Other (OTH) AF: 0.651 AC: 1371 AN: 2106

Alfa AF: 0.688 Hom.: 100275

Bravo AF: 0.635

Asia WGS AF: 0.596 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.41
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs4376071; hg19: chr3-32264991;