rs11969002

chr6-32891971-G-Achr6-32891971-G-T

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 0.129 in 152,150 control chromosomes in the GnomAD database, including 1,453 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 0.13 (1453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19603 AN: 152032 Hom.: 1447 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.129 AC: 19647 AN: 152150 Hom.: 1453 Cov.: 32 AF XY: 0.130 AC XY: 9642 AN XY: 74392

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0775 Hom.: 153

Bravo AF: 0.128

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11969002; hg19: chr6-32859748;