10-36819981-G-T

Variant names:

• chr10-36819981-G-T
• rs11817755

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 0.396 in 151,908 control chromosomes in the GnomAD database, including 12,453 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 0.40 (12453 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.396 AC: 60142 AN: 151786 Hom.: 12443 Cov.: 34

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.396 AC: 60170 AN: 151908 Hom.: 12453 Cov.: 34 AF XY: 0.404 AC XY: 30001 AN XY: 74238

African (AFR) AF: 0.360 AC: 14935 AN: 41442

American (AMR) AF: 0.445 AC: 6806 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3797 AN: 5132

South Asian (SAS) AF: 0.626 AC: 3017 AN: 4816

European-Finnish (FIN) AF: 0.394 AC: 4158 AN: 10542

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25024 AN: 67918

Other (OTH) AF: 0.390 AC: 821 AN: 2104

Alfa AF: 0.228 Hom.: 486

Bravo AF: 0.396

Asia WGS AF: 0.665 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.27
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11817755; hg19: chr10-37108909;