3-99377052-C-T

Variant names:

• chr3-99377052-C-T
• rs2200019
• ENST00000715235.1:n.51+45600C>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+45600C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,040 control chromosomes in the GnomAD database, including 7,041 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 0.30 (7041 hom., cov: 32)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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
ENSG00000243296	ENST00000715235.1	n.51+45600C>T		intron_variant	Intron 1 of 3
ENSG00000294866	ENST00000726424.1	n.175-5086G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45798 AN: 151922 Hom.: 7021 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.302 AC: 45872 AN: 152040 Hom.: 7041 Cov.: 32 AF XY: 0.302 AC XY: 22461 AN XY: 74318

African (AFR) AF: 0.336 AC: 13937 AN: 41446

American (AMR) AF: 0.275 AC: 4202 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5164

South Asian (SAS) AF: 0.312 AC: 1504 AN: 4826

European-Finnish (FIN) AF: 0.321 AC: 3395 AN: 10586

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20189 AN: 67952

Other (OTH) AF: 0.305 AC: 643 AN: 2106

Alfa AF: 0.292 Hom.: 3871

Bravo AF: 0.298

Asia WGS AF: 0.346 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2200019; hg19: chr3-99095896;