rs6936004

chr6-32889157-T-Cchr6-32889157-T-G

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 0.139 in 151,990 control chromosomes in the GnomAD database, including 1,715 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 0.14 (1715 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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: 0.138 AC: 21017 AN: 151876 Hom.: 1711 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.139 AC: 21057 AN: 151990 Hom.: 1715 Cov.: 32 AF XY: 0.139 AC XY: 10338 AN XY: 74306

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0461 Hom.: 34

Bravo AF: 0.138

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.91
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6936004; hg19: chr6-32856934;