11-48625351-G-T

Variant names:

• chr11-48625351-G-T
• rs10838987

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 0.0763 in 151,824 control chromosomes in the GnomAD database, including 633 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 0.076 (633 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 9 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 = 0.21 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0763 AC: 11573 AN: 151706 Hom.: 630 Cov.: 33

Gnomad AFR AF: 0.0189

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0763 AC: 11586 AN: 151824 Hom.: 633 Cov.: 33 AF XY: 0.0794 AC XY: 5892 AN XY: 74198

African (AFR) AF: 0.0188 AC: 781 AN: 41448

American (AMR) AF: 0.104 AC: 1588 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3466

East Asian (EAS) AF: 0.177 AC: 908 AN: 5142

South Asian (SAS) AF: 0.221 AC: 1062 AN: 4806

European-Finnish (FIN) AF: 0.0708 AC: 747 AN: 10558

Middle Eastern (MID) AF: 0.0655 AC: 19 AN: 290

European-Non Finnish (NFE) AF: 0.0891 AC: 6045 AN: 67864

Other (OTH) AF: 0.0849 AC: 179 AN: 2108

Alfa AF: 0.0814 Hom.: 873

Bravo AF: 0.0729

Asia WGS AF: 0.216 AC: 748 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs10838987; hg19: chr11-48646903;