rs11967557

Variant names:

• chr6-37403226-C-T
• rs11967557

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 0.0892 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0892 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

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.0636

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.0733

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0758

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11967557; hg19: chr6-37371002;