rs10075995

chr5-148913866-G-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 0.521 in 152,022 control chromosomes in the GnomAD database, including 21,637 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 0.52 (21637 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.655 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: 0.522 AC: 79221 AN: 151906 Hom.: 21631 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.521 AC: 79257 AN: 152022 Hom.: 21637 Cov.: 33 AF XY: 0.524 AC XY: 38913 AN XY: 74306

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.480

Alfa AF: 0.560 Hom.: 33401

Bravo AF: 0.519

Asia WGS AF: 0.564 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.57
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10075995; hg19: chr5-148293429;