11-39215482-A-G

Variant names:

• chr11-39215482-A-G
• rs2035693

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 0.57 in 151,920 control chromosomes in the GnomAD database, including 25,691 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 0.57 (25691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.570 AC: 86587 AN: 151802 Hom.: 25671 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.570 AC: 86644 AN: 151920 Hom.: 25691 Cov.: 32 AF XY: 0.574 AC XY: 42595 AN XY: 74252

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.610

Alfa AF: 0.449 Hom.: 1280

Bravo AF: 0.574

Asia WGS AF: 0.695 AC: 2409 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2035693; hg19: chr11-39237032;