11-1207997-C-T

Variant names:

• chr11-1207997-C-T
• rs28654232

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 0.366 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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.509 AC: 21133 AN: 41510

American (AMR) AF: 0.429 AC: 6565 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.250 AC: 1288 AN: 5160

South Asian (SAS) AF: 0.321 AC: 1545 AN: 4816

European-Finnish (FIN) AF: 0.263 AC: 2785 AN: 10600

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20289 AN: 67960

Other (OTH) AF: 0.339 AC: 717 AN: 2114

Alfa AF: 0.330 Hom.: 15359

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
PhyloP100		0.092

Splicing

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

Publications

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Other links and lift over

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