chr8-16066997-A-C

Variant names:

• chr8-16066997-A-C
• rs2410373

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 0.345 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.196 AC: 8111 AN: 41444

American (AMR) AF: 0.378 AC: 5761 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1396 AN: 3466

East Asian (EAS) AF: 0.191 AC: 988 AN: 5160

South Asian (SAS) AF: 0.479 AC: 2305 AN: 4812

European-Finnish (FIN) AF: 0.375 AC: 3951 AN: 10544

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.421 AC: 28635 AN: 67964

Other (OTH) AF: 0.325 AC: 686 AN: 2110

Alfa AF: 0.395 Hom.: 52351

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
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs2410373; hg19: chr8-15924506;