rs10411016

Variant names:

• chr19-7680157-G-T
• rs10411016
• ENST00000597959.1:c.163+1174G>T

Variant summary

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

The ENST00000597959.1(ENSG00000269711):​c.163+1174G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,032 control chromosomes in the GnomAD database, including 29,903 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 0.61 (29903 hom., cov: 32)
• Consequence: ENSG00000269711 ENST00000597959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 4 publications found

Genes affected

ENSG00000269711 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 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
ENSG00000269711	ENST00000597959.1	c.163+1174G>T		intron_variant	Intron 2 of 2	4		ENSP00000469811.1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92023 AN: 151914 Hom.: 29845 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.606 AC: 92131 AN: 152032 Hom.: 29903 Cov.: 32 AF XY: 0.600 AC XY: 44593 AN XY: 74294

African (AFR) AF: 0.861 AC: 35727 AN: 41502

American (AMR) AF: 0.571 AC: 8712 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2035 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2444 AN: 5160

South Asian (SAS) AF: 0.465 AC: 2236 AN: 4812

European-Finnish (FIN) AF: 0.466 AC: 4919 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34014 AN: 67958

Other (OTH) AF: 0.608 AC: 1282 AN: 2108

Alfa AF: 0.571 Hom.: 10255

Bravo AF: 0.625

Asia WGS AF: 0.503 AC: 1751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.61
PhyloP100		-2.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10411016; hg19: chr19-7745043;