8-11919395-C-T

Variant names:

• chr8-11919395-C-T
• rs10435719
• ENST00000810694.1:n.254+16702C>T

Variant summary

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

The ENST00000810694.1(ENSG00000305386):​n.254+16702C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 151,782 control chromosomes in the GnomAD database, including 21,133 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 0.49 (21133 hom., cov: 31)
• Consequence: ENSG00000305386 ENST00000810694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.661
• Publications: 8 publications found

Genes affected

ENSG00000305386 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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
ENSG00000305386	ENST00000810694.1	n.254+16702C>T		intron_variant	Intron 1 of 2
ENSG00000305386	ENST00000810695.1	n.214+16702C>T		intron_variant	Intron 1 of 1
ENSG00000305386	ENST00000810696.1	n.168+16702C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74642 AN: 151664 Hom.: 21122 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.492 AC: 74666 AN: 151782 Hom.: 21133 Cov.: 31 AF XY: 0.505 AC XY: 37478 AN XY: 74172

African (AFR) AF: 0.233 AC: 9640 AN: 41326

American (AMR) AF: 0.635 AC: 9679 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3466

East Asian (EAS) AF: 0.973 AC: 5035 AN: 5174

South Asian (SAS) AF: 0.651 AC: 3134 AN: 4812

European-Finnish (FIN) AF: 0.673 AC: 7108 AN: 10556

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37089 AN: 67886

Other (OTH) AF: 0.503 AC: 1059 AN: 2106

Alfa AF: 0.510 Hom.: 4164

Bravo AF: 0.483

Asia WGS AF: 0.775 AC: 2691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.79
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10435719; hg19: chr8-11776904;