chr11-35073939-A-G

Variant names:

• chr11-35073939-A-G
• rs2732540

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 0.599 in 152,036 control chromosomes in the GnomAD database, including 27,551 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 0.60 (27551 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.598 AC: 90915 AN: 151918 Hom.: 27514 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.599 AC: 90999 AN: 152036 Hom.: 27551 Cov.: 32 AF XY: 0.603 AC XY: 44836 AN XY: 74306

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.791

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.622

Alfa AF: 0.454 Hom.: 1283

Bravo AF: 0.603

Asia WGS AF: 0.762 AC: 2651 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732540; hg19: chr11-35095486;