rs1035961

Variant names:

• chr5-9928750-A-C
• rs1035961

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 0.0677 in 152,102 control chromosomes in the GnomAD database, including 519 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 0.068 (519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.0678 AC: 10300 AN: 151984 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0652

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

GnomAD4 genome AF: 0.0677 AC: 10303 AN: 152102 Hom.: 519 Cov.: 32 AF XY: 0.0704 AC XY: 5235 AN XY: 74330

African (AFR) AF: 0.0324 AC: 1346 AN: 41498

American (AMR) AF: 0.103 AC: 1579 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3470

East Asian (EAS) AF: 0.190 AC: 981 AN: 5160

South Asian (SAS) AF: 0.225 AC: 1082 AN: 4816

European-Finnish (FIN) AF: 0.0378 AC: 400 AN: 10572

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0629 AC: 4278 AN: 68000

Other (OTH) AF: 0.0674 AC: 142 AN: 2108

Alfa AF: 0.0674 Hom.: 1078

Bravo AF: 0.0694

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.44
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1035961; hg19: chr5-9928862;