rs1035961

Variant names:

• chr5-9928750-A-C
• rs1035961

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 0.0677 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0378

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0682 Hom.: 600

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1035961; hg19: chr5-9928862;