rs2917928

Positions:

• chr10-119556378-A-G
• chr10-119556378-A-T

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 0.414 in 152,100 control chromosomes in the GnomAD database, including 14,100 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 0.41 (14100 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62942 AN: 151980 Hom.: 14067 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.414 AC: 63027 AN: 152100 Hom.: 14100 Cov.: 33 AF XY: 0.411 AC XY: 30543 AN XY: 74352

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.437

Alfa AF: 0.299 Hom.: 1764

Bravo AF: 0.430

Asia WGS AF: 0.564 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2917928; hg19: chr10-121315890;