rs9309394

Positions:

• chr2-66781497-T-C

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 0.583 in 152,002 control chromosomes in the GnomAD database, including 27,042 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 0.58 (27042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 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: 0.583 AC: 88555 AN: 151884 Hom.: 27017 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.583 AC: 88630 AN: 152002 Hom.: 27042 Cov.: 32 AF XY: 0.572 AC XY: 42505 AN XY: 74272

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.577

Alfa AF: 0.546 Hom.: 8763

Bravo AF: 0.596

Asia WGS AF: 0.539 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9309394; hg19: chr2-67008629;