chr6-6021645-G-A

Variant names:

• chr6-6021645-G-A
• rs2326689

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 0.189 in 152,136 control chromosomes in the GnomAD database, including 2,848 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 0.19 (2848 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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: 0.189 AC: 28773 AN: 152018 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.189 AC: 28795 AN: 152136 Hom.: 2848 Cov.: 32 AF XY: 0.186 AC XY: 13830 AN XY: 74366

African (AFR) AF: 0.212 AC: 8805 AN: 41478

American (AMR) AF: 0.176 AC: 2696 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1111 AN: 5186

South Asian (SAS) AF: 0.137 AC: 658 AN: 4814

European-Finnish (FIN) AF: 0.131 AC: 1389 AN: 10586

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12643 AN: 67994

Other (OTH) AF: 0.169 AC: 356 AN: 2108

Alfa AF: 0.184 Hom.: 1612

Bravo AF: 0.196

Asia WGS AF: 0.169 AC: 592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.42
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs2326689; hg19: chr6-6021878;