rs34167775

chr10-1899958-C-A

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 0.0485 in 152,224 control chromosomes in the GnomAD database, including 241 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 0.049 (241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0623 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: 0.0486 AC: 7386 AN: 152106 Hom.: 242 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0596

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.0558

Gnomad FIN AF: 0.0717

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0485 AC: 7389 AN: 152224 Hom.: 241 Cov.: 32 AF XY: 0.0493 AC XY: 3668 AN XY: 74414

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.0631

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.0558

Gnomad4 FIN AF: 0.0717

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0589 Hom.: 26

Bravo AF: 0.0465

Asia WGS AF: 0.0440 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.48
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34167775; hg19: chr10-1942152;