10-29888959-T-C

Variant names:

• chr10-29888959-T-C
• rs3006564

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 0.606 in 152,014 control chromosomes in the GnomAD database, including 28,561 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 0.61 (28561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.606 AC: 92063 AN: 151896 Hom.: 28538 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.606 AC: 92125 AN: 152014 Hom.: 28561 Cov.: 32 AF XY: 0.606 AC XY: 45046 AN XY: 74306

African (AFR) AF: 0.717 AC: 29734 AN: 41466

American (AMR) AF: 0.550 AC: 8396 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1579 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2103 AN: 5164

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4816

European-Finnish (FIN) AF: 0.682 AC: 7204 AN: 10566

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39222 AN: 67944

Other (OTH) AF: 0.541 AC: 1142 AN: 2110

Alfa AF: 0.571 Hom.: 105332

Bravo AF: 0.601

Asia WGS AF: 0.435 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.66
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs3006564; hg19: chr10-30177888;