rs1348969

Positions:

• chr3-118347252-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000482142.5(ENSG00000243276):​n.232+149371A>G variant causes a intron, non coding transcript 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: ENST00000482142.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000482142.5	n.232+149371A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.438

Alfa AF: 0.475 Hom.: 13375

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348969; hg19: chr3-118066099;