rs17621444

Variant names:

• chr10-120062026-C-T
• rs17621444

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 0.222 in 152,140 control chromosomes in the GnomAD database, including 4,253 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 0.22 (4253 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33825 AN: 152022 Hom.: 4251 Cov.: 34

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.222 AC: 33820 AN: 152140 Hom.: 4253 Cov.: 34 AF XY: 0.221 AC XY: 16412 AN XY: 74346

African (AFR) AF: 0.123 AC: 5126 AN: 41518

American (AMR) AF: 0.197 AC: 3004 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1116 AN: 3472

East Asian (EAS) AF: 0.0436 AC: 226 AN: 5184

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2712 AN: 10570

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19495 AN: 67988

Other (OTH) AF: 0.246 AC: 520 AN: 2114

Alfa AF: 0.221 Hom.: 2631

Bravo AF: 0.214

Asia WGS AF: 0.147 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.75
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs17621444; hg19: chr10-121821538;