chr6-81821531-G-C

Variant names:

• chr6-81821531-G-C
• rs72968

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.255 AC: 10594 AN: 41494

American (AMR) AF: 0.289 AC: 4414 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3470

East Asian (EAS) AF: 0.0949 AC: 490 AN: 5164

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4826

European-Finnish (FIN) AF: 0.239 AC: 2532 AN: 10584

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15869 AN: 67970

Other (OTH) AF: 0.236 AC: 498 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs72968; hg19: chr6-82531248;