rs17101921

Variant names:

• chr10-121393781-G-A
• rs17101921

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 0.0391 in 152,204 control chromosomes in the GnomAD database, including 299 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 0.039 (299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526
• Publications: 7 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 (EAS) allele frequency at 95% confidence interval = 0.149 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: 0.0391 AC: 5939 AN: 152086 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.00650

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0178

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0282

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0391 AC: 5957 AN: 152204 Hom.: 299 Cov.: 32 AF XY: 0.0429 AC XY: 3193 AN XY: 74416

African (AFR) AF: 0.00648 AC: 269 AN: 41526

American (AMR) AF: 0.118 AC: 1804 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.158 AC: 817 AN: 5168

South Asian (SAS) AF: 0.0178 AC: 86 AN: 4820

European-Finnish (FIN) AF: 0.0879 AC: 931 AN: 10592

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0282 AC: 1918 AN: 68022

Other (OTH) AF: 0.0373 AC: 79 AN: 2116

Alfa AF: 0.0311 Hom.: 453

Bravo AF: 0.0427

Asia WGS AF: 0.0750 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.78
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs17101921; hg19: chr10-123153295;