11-1207997-C-T

Variant names:

• chr11-1207997-C-T
• rs28654232

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 0.366 in 152,120 control chromosomes in the GnomAD database, including 10,944 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 0.37 (10944 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.366 AC: 55608 AN: 152002 Hom.: 10928 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.366 AC: 55673 AN: 152120 Hom.: 10944 Cov.: 33 AF XY: 0.365 AC XY: 27164 AN XY: 74336

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.339

Alfa AF: 0.333 Hom.: 2416

Bravo AF: 0.385

Asia WGS AF: 0.327 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28654232; hg19: chr11-1229227; COSMIC: COSV65940574;