rs2991769

Variant names:

• chr10-119471927-A-G
• rs2991769

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 0.248 in 152,126 control chromosomes in the GnomAD database, including 5,330 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 0.25 (5330 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.331 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: 0.248 AC: 37770 AN: 152008 Hom.: 5329 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.248 AC: 37773 AN: 152126 Hom.: 5330 Cov.: 33 AF XY: 0.255 AC XY: 19001 AN XY: 74372

African (AFR) AF: 0.113 AC: 4694 AN: 41536

American (AMR) AF: 0.339 AC: 5178 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1434 AN: 5182

South Asian (SAS) AF: 0.249 AC: 1201 AN: 4826

European-Finnish (FIN) AF: 0.374 AC: 3936 AN: 10534

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19150 AN: 67992

Other (OTH) AF: 0.273 AC: 577 AN: 2112

Alfa AF: 0.273 Hom.: 3165

Bravo AF: 0.242

Asia WGS AF: 0.248 AC: 863 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	2.1
DANN	Benign	0.64
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2991769; hg19: chr10-121231439;