8-71653921-C-T

Variant names:

• chr8-71653921-C-T
• rs1364617
• ENST00000723932.1:n.1196-5420G>A

Variant summary

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

The ENST00000723932.1(ENSG00000294494):​n.1196-5420G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,982 control chromosomes in the GnomAD database, including 16,273 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 0.44 (16273 hom., cov: 31)
• Consequence: ENSG00000294494 ENST00000723932.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.828
• Publications: 2 publications found

Genes affected

ENSG00000294494 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 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
ENSG00000294494	ENST00000723932.1	n.1196-5420G>A		intron_variant	Intron 2 of 2
ENSG00000294494	ENST00000723933.1	n.212-5420G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66563 AN: 151864 Hom.: 16277 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.438 AC: 66577 AN: 151982 Hom.: 16273 Cov.: 31 AF XY: 0.434 AC XY: 32200 AN XY: 74254

African (AFR) AF: 0.217 AC: 8991 AN: 41476

American (AMR) AF: 0.439 AC: 6705 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2722 AN: 5152

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4810

European-Finnish (FIN) AF: 0.536 AC: 5652 AN: 10546

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.558 AC: 37919 AN: 67954

Other (OTH) AF: 0.420 AC: 885 AN: 2106

Alfa AF: 0.509 Hom.: 4287

Bravo AF: 0.427

Asia WGS AF: 0.382 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.41
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1364617; hg19: chr8-72566156;