chr8-9552985-C-T

Variant names:

• chr8-9552985-C-T
• rs10503380

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 0.255 in 151,928 control chromosomes in the GnomAD database, including 5,179 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 0.26 (5179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 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: 0.255 AC: 38723 AN: 151810 Hom.: 5157 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.255 AC: 38783 AN: 151928 Hom.: 5179 Cov.: 32 AF XY: 0.261 AC XY: 19389 AN XY: 74234

African (AFR) AF: 0.276 AC: 11431 AN: 41420

American (AMR) AF: 0.200 AC: 3047 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3464

East Asian (EAS) AF: 0.371 AC: 1919 AN: 5166

South Asian (SAS) AF: 0.304 AC: 1464 AN: 4814

European-Finnish (FIN) AF: 0.375 AC: 3949 AN: 10524

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15787 AN: 67966

Other (OTH) AF: 0.222 AC: 469 AN: 2108

Alfa AF: 0.230 Hom.: 3307

Bravo AF: 0.245

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10503380; hg19: chr8-9410495;