rs991035

Variant names:

• chr5-111063335-G-A
• rs991035

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 0.658 in 152,022 control chromosomes in the GnomAD database, including 34,685 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 0.66 (34685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 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: 0.658 AC: 99910 AN: 151904 Hom.: 34633 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.658 AC: 100014 AN: 152022 Hom.: 34685 Cov.: 32 AF XY: 0.657 AC XY: 48826 AN XY: 74282

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.661

Alfa AF: 0.565 Hom.: 35572

Bravo AF: 0.680

Asia WGS AF: 0.699 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs991035; hg19: chr5-110399033;