10-115987462-G-C

Variant names:

• chr10-115987462-G-C
• rs180683

Variant summary

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

The variant allele was found at a frequency of 0.976 in 152,268 control chromosomes in the GnomAD database, including 72,514 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 0.98 (72514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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

Frequencies

GnomAD3 genomes AF: 0.976 AC: 148481 AN: 152150 Hom.: 72465 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.984

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.975

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

GnomAD4 genome AF: 0.976 AC: 148587 AN: 152268 Hom.: 72514 Cov.: 31 AF XY: 0.977 AC XY: 72741 AN XY: 74452

African (AFR) AF: 0.955 AC: 39684 AN: 41542

American (AMR) AF: 0.984 AC: 15046 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.986 AC: 3423 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5101 AN: 5164

South Asian (SAS) AF: 0.968 AC: 4666 AN: 4820

European-Finnish (FIN) AF: 0.997 AC: 10589 AN: 10618

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66828 AN: 68038

Other (OTH) AF: 0.974 AC: 2061 AN: 2116

Alfa AF: 0.985 Hom.: 3423

Bravo AF: 0.975

Asia WGS AF: 0.956 AC: 3325 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.16
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs180683; hg19: chr10-117746973;