rs991035

Variant names:

• chr5-111063335-G-A
• rs991035
• ENST00000743602.1:n.29+3100C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000743602.1(ENSG00000296915):​n.29+3100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000296915 ENST00000743602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.762
• Publications: 4 publications found

Genes affected

ENSG00000296915 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743602.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296915	ENST00000743602.1		n.29+3100C>T		intron	N/A

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

African (AFR) AF: 0.891 AC: 36994 AN: 41504

American (AMR) AF: 0.648 AC: 9892 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2093 AN: 3470

East Asian (EAS) AF: 0.746 AC: 3847 AN: 5158

South Asian (SAS) AF: 0.600 AC: 2896 AN: 4824

European-Finnish (FIN) AF: 0.513 AC: 5411 AN: 10552

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36688 AN: 67948

Other (OTH) AF: 0.661 AC: 1395 AN: 2110

Alfa AF: 0.580 Hom.: 93502

Bravo AF: 0.680

Asia WGS AF: 0.699 AC: 2431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.38
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs991035; hg19: chr5-110399033;