rs10075995

Variant names:

• chr5-148913866-G-A
• rs10075995

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 0.521 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.357 AC: 14779 AN: 41454

American (AMR) AF: 0.633 AC: 9665 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3470

East Asian (EAS) AF: 0.673 AC: 3481 AN: 5170

South Asian (SAS) AF: 0.441 AC: 2120 AN: 4806

European-Finnish (FIN) AF: 0.607 AC: 6416 AN: 10564

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.579 AC: 39379 AN: 67966

Other (OTH) AF: 0.480 AC: 1013 AN: 2112

Alfa AF: 0.556 Hom.: 41612

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10075995; hg19: chr5-148293429;