11-122606317-T-C

Variant names:

• chr11-122606317-T-C
• rs12420917

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 0.35 in 152,002 control chromosomes in the GnomAD database, including 9,669 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 0.35 (9669 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 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: 0.350 AC: 53217 AN: 151884 Hom.: 9659 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.350 AC: 53271 AN: 152002 Hom.: 9669 Cov.: 32 AF XY: 0.356 AC XY: 26414 AN XY: 74280

African (AFR) AF: 0.274 AC: 11372 AN: 41470

American (AMR) AF: 0.403 AC: 6159 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1471 AN: 3472

East Asian (EAS) AF: 0.525 AC: 2714 AN: 5174

South Asian (SAS) AF: 0.343 AC: 1652 AN: 4812

European-Finnish (FIN) AF: 0.402 AC: 4245 AN: 10556

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24449 AN: 67938

Other (OTH) AF: 0.340 AC: 718 AN: 2110

Alfa AF: 0.355 Hom.: 40611

Bravo AF: 0.347

Asia WGS AF: 0.417 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.33
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs12420917; hg19: chr11-122477025;