rs11970254

Variant names:

• chr6-66939323-G-T
• rs11970254

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 0.292 in 151,760 control chromosomes in the GnomAD database, including 6,717 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 0.29 (6717 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.292 AC: 44253 AN: 151642 Hom.: 6720 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.292 AC: 44265 AN: 151760 Hom.: 6717 Cov.: 33 AF XY: 0.288 AC XY: 21327 AN XY: 74132

African (AFR) AF: 0.216 AC: 8945 AN: 41418

American (AMR) AF: 0.224 AC: 3416 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 831 AN: 3466

East Asian (EAS) AF: 0.287 AC: 1484 AN: 5168

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4820

European-Finnish (FIN) AF: 0.359 AC: 3784 AN: 10530

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23848 AN: 67802

Other (OTH) AF: 0.265 AC: 560 AN: 2110

Alfa AF: 0.319 Hom.: 13260

Bravo AF: 0.279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.20
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs11970254; hg19: chr6-67649216;