11-38488150-A-T

Variant names:

• chr11-38488150-A-T
• rs7930841

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 0.58 in 151,992 control chromosomes in the GnomAD database, including 25,830 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 0.58 (25830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.750
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.605 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: 0.580 AC: 88054 AN: 151872 Hom.: 25823 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.580 AC: 88090 AN: 151992 Hom.: 25830 Cov.: 32 AF XY: 0.573 AC XY: 42590 AN XY: 74280

African (AFR) AF: 0.597 AC: 24734 AN: 41452

American (AMR) AF: 0.476 AC: 7271 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1990 AN: 3472

East Asian (EAS) AF: 0.400 AC: 2066 AN: 5164

South Asian (SAS) AF: 0.513 AC: 2469 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6120 AN: 10548

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41461 AN: 67964

Other (OTH) AF: 0.560 AC: 1184 AN: 2116

Alfa AF: 0.503 Hom.: 1464

Bravo AF: 0.571

Asia WGS AF: 0.484 AC: 1684 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	3.0
DANN	Benign	0.47
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs7930841; hg19: chr11-38509700;