rs963170

Variant names:

• chr1-119018045-A-C
• rs963170

Your query was ambiguous. Multiple possible variants found:

• chr1-119018045-A-C
• chr1-119018045-A-T

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 0.17 in 152,258 control chromosomes in the GnomAD database, including 3,357 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 0.17 (3357 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 6 publications found

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 = 0.476 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: 0.171 AC: 25942 AN: 152140 Hom.: 3350 Cov.: 33

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.170 AC: 25943 AN: 152258 Hom.: 3357 Cov.: 33 AF XY: 0.177 AC XY: 13202 AN XY: 74442

African (AFR) AF: 0.0428 AC: 1778 AN: 41580

American (AMR) AF: 0.368 AC: 5632 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 387 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2550 AN: 5180

South Asian (SAS) AF: 0.131 AC: 632 AN: 4830

European-Finnish (FIN) AF: 0.240 AC: 2542 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11948 AN: 68004

Other (OTH) AF: 0.174 AC: 367 AN: 2114

Alfa AF: 0.0932 Hom.: 160

Bravo AF: 0.181

Asia WGS AF: 0.274 AC: 953 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	1.3
DANN	Benign	0.67
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs963170; hg19: chr1-119560668;