chr11-48625351-G-T

Variant names:

• chr11-48625351-G-T
• rs10838987

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0763 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

Gnomad4 AFR AF: 0.0188

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.0708

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.0849

Alfa AF: 0.0812 Hom.: 614

Bravo AF: 0.0729

Asia WGS AF: 0.216 AC: 748 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10838987; hg19: chr11-48646903;