10-52393269-A-G

Variant names:

• chr10-52393269-A-G
• rs1194661
• ENST00000766677.1:n.81+660T>C

Variant summary

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

The ENST00000766677.1(ENSG00000299824):​n.81+660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 151,608 control chromosomes in the GnomAD database, including 38,366 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 0.69 (38366 hom., cov: 31)
• Consequence: ENSG00000299824 ENST00000766677.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 3 publications found

Genes affected

ENSG00000299824 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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
ENSG00000299824	ENST00000766677.1	n.81+660T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.693 AC: 104944 AN: 151494 Hom.: 38295 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.693 AC: 105071 AN: 151608 Hom.: 38366 Cov.: 31 AF XY: 0.691 AC XY: 51144 AN XY: 74036

African (AFR) AF: 0.922 AC: 38166 AN: 41388

American (AMR) AF: 0.609 AC: 9271 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4778 AN: 5134

South Asian (SAS) AF: 0.646 AC: 3114 AN: 4818

European-Finnish (FIN) AF: 0.581 AC: 6045 AN: 10406

Middle Eastern (MID) AF: 0.569 AC: 164 AN: 288

European-Non Finnish (NFE) AF: 0.589 AC: 39951 AN: 67872

Other (OTH) AF: 0.636 AC: 1334 AN: 2096

Alfa AF: 0.648 Hom.: 3909

Bravo AF: 0.704

Asia WGS AF: 0.834 AC: 2897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.48
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1194661; hg19: chr10-54153029;