rs2294405

Variant names:

• chr6-98844260-G-A
• rs2294405

Your query was ambiguous. Multiple possible variants found:

• chr6-98844260-G-A
• chr6-98844260-G-C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.306 in 152,188 control chromosomes in the GnomAD database, including 7,972 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 0.31 (7972 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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: 0.306 AC: 46542 AN: 152070 Hom.: 7962 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.306 AC: 46572 AN: 152188 Hom.: 7972 Cov.: 33 AF XY: 0.310 AC XY: 23044 AN XY: 74400

African (AFR) AF: 0.205 AC: 8521 AN: 41534

American (AMR) AF: 0.370 AC: 5658 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 817 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3637 AN: 5170

South Asian (SAS) AF: 0.378 AC: 1822 AN: 4826

European-Finnish (FIN) AF: 0.322 AC: 3406 AN: 10586

Middle Eastern (MID) AF: 0.228 AC: 66 AN: 290

European-Non Finnish (NFE) AF: 0.318 AC: 21628 AN: 67994

Other (OTH) AF: 0.297 AC: 628 AN: 2114

Alfa AF: 0.307 Hom.: 5578

Bravo AF: 0.307

Asia WGS AF: 0.497 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	20
DANN	Benign	0.87
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs2294405; hg19: chr6-99292136; COSMIC: COSV60253819;