chr6-81068200-G-A

Variant names:

• chr6-81068200-G-A
• rs310389

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 0.438 in 152,026 control chromosomes in the GnomAD database, including 15,790 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 0.44 (15790 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66558 AN: 151906 Hom.: 15790 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.438 AC: 66560 AN: 152026 Hom.: 15790 Cov.: 32 AF XY: 0.432 AC XY: 32117 AN XY: 74296

African (AFR) AF: 0.249 AC: 10326 AN: 41484

American (AMR) AF: 0.475 AC: 7250 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1534 AN: 5176

South Asian (SAS) AF: 0.382 AC: 1840 AN: 4820

European-Finnish (FIN) AF: 0.461 AC: 4862 AN: 10544

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.546 AC: 37107 AN: 67950

Other (OTH) AF: 0.445 AC: 939 AN: 2108

Alfa AF: 0.494 Hom.: 3299

Bravo AF: 0.431

Asia WGS AF: 0.312 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs310389; hg19: chr6-81777917;