chr3-99375946-C-T

Variant names:

• chr3-99375946-C-T
• rs2700586
• ENST00000715235.1:n.51+44494C>T

Variant summary

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

The ENST00000715235.1(ENSG00000243296):​n.51+44494C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,596 control chromosomes in the GnomAD database, including 10,955 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 0.35 (10955 hom., cov: 31)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• Publications: 2 publications found

Genes affected

ENSG00000243296 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243296	ENST00000715235.1		n.51+44494C>T		intron	N/A
	ENSG00000294866	ENST00000726424.1		n.175-3980G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53372 AN: 151476 Hom.: 10918 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.353 AC: 53464 AN: 151596 Hom.: 10955 Cov.: 31 AF XY: 0.351 AC XY: 26025 AN XY: 74058

African (AFR) AF: 0.576 AC: 23763 AN: 41262

American (AMR) AF: 0.287 AC: 4377 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3466

East Asian (EAS) AF: 0.316 AC: 1616 AN: 5118

South Asian (SAS) AF: 0.350 AC: 1680 AN: 4804

European-Finnish (FIN) AF: 0.288 AC: 3028 AN: 10506

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17559 AN: 67904

Other (OTH) AF: 0.327 AC: 689 AN: 2108

Alfa AF: 0.275 Hom.: 4688

Bravo AF: 0.359

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2700586; hg19: chr3-99094790;