rs1348969

Variant names:

• chr3-118347252-T-C
• rs1348969
• ENST00000482142.5:n.232+149371A>G

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+149371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,988 control chromosomes in the GnomAD database, including 13,768 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 0.41 (13768 hom., cov: 31)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 5 publications found

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 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
ENSG00000243276	ENST00000482142.5	n.232+149371A>G		intron_variant	Intron 3 of 6	5
ENSG00000243276	ENST00000833975.1	n.449-4978A>G		intron_variant	Intron 5 of 5
ENSG00000243276	ENST00000833976.1	n.350-4978A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62173 AN: 151868 Hom.: 13771 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.409 AC: 62190 AN: 151988 Hom.: 13768 Cov.: 31 AF XY: 0.408 AC XY: 30310 AN XY: 74262

African (AFR) AF: 0.242 AC: 10057 AN: 41486

American (AMR) AF: 0.433 AC: 6610 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1949 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1564 AN: 5150

South Asian (SAS) AF: 0.402 AC: 1936 AN: 4818

European-Finnish (FIN) AF: 0.429 AC: 4527 AN: 10550

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33969 AN: 67940

Other (OTH) AF: 0.438 AC: 926 AN: 2116

Alfa AF: 0.470 Hom.: 18324

Bravo AF: 0.403

Asia WGS AF: 0.333 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.74
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1348969; hg19: chr3-118066099;