chr10-119556378-A-G

Variant names:

• chr10-119556378-A-G
• rs2917928

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 0.414 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.558 AC: 23157 AN: 41480

American (AMR) AF: 0.394 AC: 6021 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3470

East Asian (EAS) AF: 0.705 AC: 3646 AN: 5174

South Asian (SAS) AF: 0.445 AC: 2147 AN: 4824

European-Finnish (FIN) AF: 0.256 AC: 2709 AN: 10588

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22897 AN: 67972

Other (OTH) AF: 0.437 AC: 922 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs2917928; hg19: chr10-121315890;