10-27503160-A-G

Variant names:

• chr10-27503160-A-G
• rs10764698

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 0.503 in 151,980 control chromosomes in the GnomAD database, including 19,288 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 0.50 (19288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76354 AN: 151862 Hom.: 19285 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.503 AC: 76388 AN: 151980 Hom.: 19288 Cov.: 32 AF XY: 0.503 AC XY: 37363 AN XY: 74276

African (AFR) AF: 0.508 AC: 21069 AN: 41442

American (AMR) AF: 0.435 AC: 6642 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2046 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2367 AN: 5146

South Asian (SAS) AF: 0.520 AC: 2508 AN: 4824

European-Finnish (FIN) AF: 0.531 AC: 5596 AN: 10536

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34476 AN: 67958

Other (OTH) AF: 0.478 AC: 1011 AN: 2114

Alfa AF: 0.503 Hom.: 23688

Bravo AF: 0.493

Asia WGS AF: 0.477 AC: 1656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.4
DANN	Benign	0.75
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs10764698; hg19: chr10-27792089;