rs2326689

Positions:

• chr6-6021645-G-A
• chr6-6021645-G-T

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 0.189 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.169

Alfa AF: 0.183 Hom.: 1453

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2326689; hg19: chr6-6021878;