chr10-100709645-C-A

Variant names:

• chr10-100709645-C-A
• rs6584389

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 0.44 in 151,964 control chromosomes in the GnomAD database, including 15,453 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 0.44 (15453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.509 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: 0.440 AC: 66879 AN: 151846 Hom.: 15442 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.440 AC: 66923 AN: 151964 Hom.: 15453 Cov.: 32 AF XY: 0.438 AC XY: 32557 AN XY: 74270

African (AFR) AF: 0.312 AC: 12910 AN: 41436

American (AMR) AF: 0.460 AC: 7025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1869 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1681 AN: 5130

South Asian (SAS) AF: 0.364 AC: 1751 AN: 4816

European-Finnish (FIN) AF: 0.512 AC: 5410 AN: 10572

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34861 AN: 67940

Other (OTH) AF: 0.453 AC: 957 AN: 2112

Alfa AF: 0.487 Hom.: 7995

Bravo AF: 0.431

Asia WGS AF: 0.352 AC: 1229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	19
DANN	Benign	0.53
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6584389; hg19: chr10-102469402;