10-8696945-G-T

Variant names:

• chr10-8696945-G-T
• rs7898455

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 0.27 in 151,892 control chromosomes in the GnomAD database, including 6,151 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 0.27 (6151 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 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: 0.270 AC: 41002 AN: 151774 Hom.: 6132 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.270 AC: 41038 AN: 151892 Hom.: 6151 Cov.: 31 AF XY: 0.272 AC XY: 20214 AN XY: 74214

African (AFR) AF: 0.128 AC: 5310 AN: 41452

American (AMR) AF: 0.319 AC: 4864 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1828 AN: 5140

South Asian (SAS) AF: 0.280 AC: 1347 AN: 4808

European-Finnish (FIN) AF: 0.332 AC: 3493 AN: 10524

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22116 AN: 67938

Other (OTH) AF: 0.292 AC: 618 AN: 2114

Alfa AF: 0.307 Hom.: 31729

Bravo AF: 0.263

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.63
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs7898455; hg19: chr10-8738908;