rs11967684

Positions:

• chr6-31231989-G-A

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 0.424 in 152,072 control chromosomes in the GnomAD database, including 14,417 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 0.42 (14417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64368 AN: 151958 Hom.: 14396 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.424 AC: 64431 AN: 152072 Hom.: 14417 Cov.: 32 AF XY: 0.426 AC XY: 31662 AN XY: 74338

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.415

Alfa AF: 0.391 Hom.: 2967

Bravo AF: 0.430

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11967684; hg19: chr6-31199766;