chr10-119474551-C-T

Variant names:

• chr10-119474551-C-T
• rs2991770

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 0.249 in 152,220 control chromosomes in the GnomAD database, including 5,415 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 (5415 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 5 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.335 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: 0.249 AC: 37841 AN: 152102 Hom.: 5415 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.249 AC: 37845 AN: 152220 Hom.: 5415 Cov.: 33 AF XY: 0.257 AC XY: 19092 AN XY: 74416

African (AFR) AF: 0.107 AC: 4436 AN: 41538

American (AMR) AF: 0.342 AC: 5240 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1494 AN: 5178

South Asian (SAS) AF: 0.250 AC: 1203 AN: 4818

European-Finnish (FIN) AF: 0.374 AC: 3962 AN: 10594

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19345 AN: 67998

Other (OTH) AF: 0.275 AC: 581 AN: 2116

Alfa AF: 0.280 Hom.: 20165

Bravo AF: 0.241

Asia WGS AF: 0.253 AC: 880 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	2.4
DANN	Benign	0.44
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs2991770; hg19: chr10-121234063;