rs2345276

Variant names:

• chr4-157804947-G-A
• rs2345276
• ENST00000652341.2:n.455+18855C>T

Variant summary

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

The ENST00000652341.2(ENSG00000287226):​n.455+18855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 152,036 control chromosomes in the GnomAD database, including 1,160 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 0.073 (1160 hom., cov: 32)
• Consequence: ENSG00000287226 ENST00000652341.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 0 publications found

Genes affected

ENSG00000287226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377509	XR_007058347.1	n.860+304C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287226	ENST00000652341.2	n.455+18855C>T		intron_variant	Intron 1 of 2
ENSG00000287226	ENST00000809819.1	n.445-1246C>T		intron_variant	Intron 3 of 3
ENSG00000287226	ENST00000809820.1	n.311-1246C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10985 AN: 151918 Hom.: 1153 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0464

Gnomad EAS AF: 0.000967

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00708

Gnomad OTH AF: 0.0585

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

GnomAD4 genome AF: 0.0725 AC: 11028 AN: 152036 Hom.: 1160 Cov.: 32 AF XY: 0.0701 AC XY: 5208 AN XY: 74314

African (AFR) AF: 0.229 AC: 9512 AN: 41464

American (AMR) AF: 0.0435 AC: 663 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0464 AC: 161 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5160

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4828

European-Finnish (FIN) AF: 0.00396 AC: 42 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00709 AC: 482 AN: 67938

Other (OTH) AF: 0.0598 AC: 126 AN: 2108

Alfa AF: 0.0349 Hom.: 246

Bravo AF: 0.0828

Asia WGS AF: 0.0210 AC: 72 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.60
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2345276; hg19: chr4-158726099;