rs2410373

Positions:

• chr8-16066997-A-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 0.345 in 151,962 control chromosomes in the GnomAD database, including 9,862 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 0.34 (9862 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52361 AN: 151844 Hom.: 9857 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.345 AC: 52375 AN: 151962 Hom.: 9862 Cov.: 31 AF XY: 0.344 AC XY: 25572 AN XY: 74258

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.325

Alfa AF: 0.404 Hom.: 25638

Bravo AF: 0.329

Asia WGS AF: 0.285 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2410373; hg19: chr8-15924506;