rs10792438

Variant names:

• chr11-64535054-G-A
• rs10792438

Your query was ambiguous. Multiple possible variants found:

• chr11-64535054-G-A
• chr11-64535054-G-C
• chr11-64535054-G-T

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 0.281 in 152,152 control chromosomes in the GnomAD database, including 7,665 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 0.28 (7665 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42719 AN: 152032 Hom.: 7645 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.281 AC: 42782 AN: 152152 Hom.: 7665 Cov.: 33 AF XY: 0.287 AC XY: 21330 AN XY: 74398

African (AFR) AF: 0.446 AC: 18497 AN: 41466

American (AMR) AF: 0.367 AC: 5615 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3257 AN: 5182

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4826

European-Finnish (FIN) AF: 0.200 AC: 2121 AN: 10602

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10304 AN: 68000

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.192 Hom.: 6045

Bravo AF: 0.299

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.2
DANN	Benign	0.83
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10792438; hg19: chr11-64302526;