ENST00000722615.1:n.681+7571A>G

Variant names:

• chr3-86215133-T-C
• rs2175671
• ENST00000722615.1:n.681+7571A>G

Variant summary

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

The ENST00000722615.1(ENSG00000239767):​n.681+7571A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,678 control chromosomes in the GnomAD database, including 33,788 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 0.66 (33788 hom., cov: 32)
• Consequence: ENSG00000239767 ENST00000722615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880
• Publications: 2 publications found

Genes affected

ENSG00000239767 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723364	NR_188544.1	n.679+7571A>G		intron_variant	Intron 4 of 4
LOC102723364	NR_188545.1	n.597+7571A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239767	ENST00000722615.1	n.681+7571A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.660 AC: 99962 AN: 151560 Hom.: 33758 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.659 AC: 100031 AN: 151678 Hom.: 33788 Cov.: 32 AF XY: 0.656 AC XY: 48583 AN XY: 74106

African (AFR) AF: 0.536 AC: 22165 AN: 41370

American (AMR) AF: 0.638 AC: 9681 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2274 AN: 3464

East Asian (EAS) AF: 0.492 AC: 2538 AN: 5154

South Asian (SAS) AF: 0.503 AC: 2417 AN: 4808

European-Finnish (FIN) AF: 0.809 AC: 8539 AN: 10550

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50268 AN: 67840

Other (OTH) AF: 0.655 AC: 1384 AN: 2112

Alfa AF: 0.711 Hom.: 41124

Bravo AF: 0.643

Asia WGS AF: 0.519 AC: 1782 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.5
DANN	Benign	0.89
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs2175671; hg19: chr3-86264283;