11-35865369-T-C

Variant names:

• chr11-35865369-T-C
• rs684909

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 0.569 in 152,070 control chromosomes in the GnomAD database, including 25,209 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 (25209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

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 (AMR) allele frequency at 95% confidence interval = 0.632 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: 0.569 AC: 86494 AN: 151952 Hom.: 25200 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.569 AC: 86548 AN: 152070 Hom.: 25209 Cov.: 32 AF XY: 0.572 AC XY: 42555 AN XY: 74334

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.622

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.557

Alfa AF: 0.597 Hom.: 40144

Bravo AF: 0.562

Asia WGS AF: 0.570 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs684909; hg19: chr11-35886919; COSMIC: COSV73331315;