rs9294269

Variant names:

• chr6-63627392-A-C
• rs9294269

Your query was ambiguous. Multiple possible variants found:

• chr6-63627392-A-C
• chr6-63627392-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 0.465 in 151,958 control chromosomes in the GnomAD database, including 18,219 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 0.47 (18219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 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: 0.466 AC: 70725 AN: 151840 Hom.: 18224 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.465 AC: 70714 AN: 151958 Hom.: 18219 Cov.: 32 AF XY: 0.469 AC XY: 34832 AN XY: 74282

African (AFR) AF: 0.234 AC: 9715 AN: 41446

American (AMR) AF: 0.467 AC: 7121 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3472

East Asian (EAS) AF: 0.547 AC: 2826 AN: 5168

South Asian (SAS) AF: 0.504 AC: 2424 AN: 4812

European-Finnish (FIN) AF: 0.629 AC: 6631 AN: 10538

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38168 AN: 67942

Other (OTH) AF: 0.510 AC: 1078 AN: 2112

Alfa AF: 0.395 Hom.: 1534

Bravo AF: 0.443

Asia WGS AF: 0.542 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.80
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs9294269; hg19: chr6-64337297;