11-1205839-C-T

Variant names:

• chr11-1205839-C-T
• rs35671223

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 0.323 in 151,976 control chromosomes in the GnomAD database, including 8,484 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 0.32 (8484 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 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: 0.323 AC: 49028 AN: 151858 Hom.: 8444 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.323 AC: 49120 AN: 151976 Hom.: 8484 Cov.: 32 AF XY: 0.317 AC XY: 23514 AN XY: 74270

African (AFR) AF: 0.430 AC: 17826 AN: 41416

American (AMR) AF: 0.235 AC: 3585 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1095 AN: 3472

East Asian (EAS) AF: 0.111 AC: 571 AN: 5164

South Asian (SAS) AF: 0.166 AC: 801 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2686 AN: 10562

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21491 AN: 67946

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.204 Hom.: 515

Bravo AF: 0.326

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.47
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs35671223; hg19: chr11-1227069;