rs11967557

Variant names:

• chr6-37403226-C-T
• rs11967557

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 0.0892 in 152,202 control chromosomes in the GnomAD database, including 659 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 0.089 (659 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0994 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13572 AN: 152084 Hom.: 658 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0637

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.0163

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0892 AC: 13576 AN: 152202 Hom.: 659 Cov.: 32 AF XY: 0.0889 AC XY: 6614 AN XY: 74422

African (AFR) AF: 0.0866 AC: 3597 AN: 41518

American (AMR) AF: 0.0636 AC: 972 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3466

East Asian (EAS) AF: 0.0164 AC: 85 AN: 5194

South Asian (SAS) AF: 0.0733 AC: 354 AN: 4828

European-Finnish (FIN) AF: 0.123 AC: 1298 AN: 10586

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6893 AN: 68000

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.100 Hom.: 93

Bravo AF: 0.0848

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.4
DANN	Benign	0.85
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs11967557; hg19: chr6-37371002;