rs2395309

Variant names:

• chr6-33058469-A-G
• rs2395309

Your query was ambiguous. Multiple possible variants found:

• chr6-33058469-A-G
• chr6-33058469-A-T

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 0.287 in 151,484 control chromosomes in the GnomAD database, including 8,432 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 0.29 (8432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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: 0.287 AC: 43486 AN: 151372 Hom.: 8413 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.287 AC: 43534 AN: 151484 Hom.: 8432 Cov.: 31 AF XY: 0.285 AC XY: 21069 AN XY: 74044

African (AFR) AF: 0.495 AC: 20382 AN: 41188

American (AMR) AF: 0.244 AC: 3712 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3462

East Asian (EAS) AF: 0.688 AC: 3549 AN: 5160

South Asian (SAS) AF: 0.339 AC: 1626 AN: 4792

European-Finnish (FIN) AF: 0.101 AC: 1067 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11803 AN: 67756

Other (OTH) AF: 0.305 AC: 641 AN: 2100

Alfa AF: 0.240 Hom.: 8089

Bravo AF: 0.308

Asia WGS AF: 0.452 AC: 1571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.8
DANN	Benign	0.31
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2395309; hg19: chr6-33026246;