10-2734506-A-T

Variant names:

• chr10-2734506-A-T
• rs79619559

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.019 in 152,286 control chromosomes in the GnomAD database, including 47 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 0.019 (47 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.019 (2888/152286) while in subpopulation AFR AF = 0.0386 (1606/41560). AF 95% confidence interval is 0.0371. There are 47 homozygotes in GnomAd4. There are 1415 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0190 AC: 2890 AN: 152168 Hom.: 47 Cov.: 32

Gnomad AFR AF: 0.0387

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.00726

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0190 AC: 2888 AN: 152286 Hom.: 47 Cov.: 32 AF XY: 0.0190 AC XY: 1415 AN XY: 74468

African (AFR) AF: 0.0386 AC: 1606 AN: 41560

American (AMR) AF: 0.0171 AC: 262 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5176

South Asian (SAS) AF: 0.00726 AC: 35 AN: 4818

European-Finnish (FIN) AF: 0.00188 AC: 20 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 684 AN: 68020

Other (OTH) AF: 0.0175 AC: 37 AN: 2116

Alfa AF: 0.0127 Hom.: 4

Bravo AF: 0.0205

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.6
DANN	Benign	0.80
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs79619559; hg19: chr10-2776698;