10-29002969-A-T

Variant names:

• chr10-29002969-A-T
• rs1612122

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 0.473 in 151,778 control chromosomes in the GnomAD database, including 17,035 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 0.47 (17035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71700 AN: 151662 Hom.: 17022 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.473 AC: 71747 AN: 151778 Hom.: 17035 Cov.: 31 AF XY: 0.474 AC XY: 35130 AN XY: 74170

African (AFR) AF: 0.436 AC: 18034 AN: 41364

American (AMR) AF: 0.480 AC: 7323 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3464

East Asian (EAS) AF: 0.343 AC: 1773 AN: 5166

South Asian (SAS) AF: 0.519 AC: 2503 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5500 AN: 10478

Middle Eastern (MID) AF: 0.535 AC: 154 AN: 288

European-Non Finnish (NFE) AF: 0.493 AC: 33472 AN: 67922

Other (OTH) AF: 0.469 AC: 987 AN: 2106

Alfa AF: 0.487 Hom.: 2236

Bravo AF: 0.467

Asia WGS AF: 0.408 AC: 1419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.73
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1612122; hg19: chr10-29291898;