3-148038899-G-T

Position:

• chr3-148038899-G-T

Variant summary

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

The ENST00000649594.1(ENSG00000285798):​n.380+339C>A 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 0.644 in 151,578 control chromosomes in the GnomAD database, including 32,756 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 0.64 (32756 hom., cov: 31)
• Consequence: ENST00000649594.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000649594.1	n.380+339C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97467 AN: 151460 Hom.: 32695 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.644 AC: 97592 AN: 151578 Hom.: 32756 Cov.: 31 AF XY: 0.654 AC XY: 48433 AN XY: 74064

Gnomad4 AFR AF: 0.813

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.635

Alfa AF: 0.561 Hom.: 33429

Bravo AF: 0.648

Asia WGS AF: 0.798 AC: 2760 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1841770; hg19: chr3-147756686;