rs17621444

Variant names:

• chr10-120062026-C-T
• rs17621444

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.223 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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.0436

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.246

Alfa AF: 0.257 Hom.: 1130

Bravo AF: 0.214

Asia WGS AF: 0.147 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17621444; hg19: chr10-121821538;