rs991035

Positions:

• chr5-111063335-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 0.658 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;