chr6-81821531-G-C

Position:

• chr6-81821531-G-C

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 0.238 in 152,098 control chromosomes in the GnomAD database, including 4,513 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 0.24 (4513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 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: 0.238 AC: 36227 AN: 151980 Hom.: 4512 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.238 AC: 36254 AN: 152098 Hom.: 4513 Cov.: 32 AF XY: 0.238 AC XY: 17732 AN XY: 74352

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.236

Alfa AF: 0.124 Hom.: 224

Bravo AF: 0.240

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72968; hg19: chr6-82531248;