chr8-141622215-T-C

Variant names:

• chr8-141622215-T-C
• rs13263959
• ENST00000673717.1:n.2021+9355T>C

Variant summary

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

The ENST00000673717.1(ENSG00000287677):​n.2021+9355T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,226 control chromosomes in the GnomAD database, including 45,596 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 0.77 (45596 hom., cov: 34)
• Consequence: ENSG00000287677 ENST00000673717.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 11 publications found

Genes affected

ENSG00000287677 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 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
ENSG00000287677	ENST00000673717.1	n.2021+9355T>C		intron_variant	Intron 4 of 8
ENSG00000287677	ENST00000673759.1	n.2006+9355T>C		intron_variant	Intron 4 of 5
ENSG00000287677	ENST00000673982.1	n.1993+9355T>C		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117221 AN: 152108 Hom.: 45542 Cov.: 34

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.771 AC: 117337 AN: 152226 Hom.: 45596 Cov.: 34 AF XY: 0.765 AC XY: 56958 AN XY: 74416

African (AFR) AF: 0.816 AC: 33913 AN: 41546

American (AMR) AF: 0.677 AC: 10368 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2197 AN: 3466

East Asian (EAS) AF: 0.635 AC: 3285 AN: 5170

South Asian (SAS) AF: 0.612 AC: 2951 AN: 4820

European-Finnish (FIN) AF: 0.814 AC: 8636 AN: 10604

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53577 AN: 68004

Other (OTH) AF: 0.719 AC: 1518 AN: 2110

Alfa AF: 0.768 Hom.: 104534

Bravo AF: 0.767

Asia WGS AF: 0.626 AC: 2177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.40
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs13263959; hg19: chr8-142632315;