3-109810703-T-C

Position:

• chr3-109810703-T-C

Variant summary

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

The ENST00000485384.1(ENSG00000242029):​n.104T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,746 control chromosomes in the GnomAD database, including 25,606 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 0.58 (25602 hom., cov: 30)
  • Exomes 𝑓: 0.72 (4 hom.)
• Consequence: ENST00000485384.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906267	XR_007096002.1	n.155-25390T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000485384.1	n.104T>C		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87829 AN: 151610 Hom.: 25554 Cov.: 30

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.560

GnomAD4 exome AF: 0.722 AC: 13 AN: 18 Hom.: 4 Cov.: 0 AF XY: 0.750 AC XY: 9 AN XY: 12

Gnomad4 NFE exome AF: 0.722

GnomAD4 genome AF: 0.580 AC: 87941 AN: 151728 Hom.: 25602 Cov.: 30 AF XY: 0.582 AC XY: 43128 AN XY: 74110

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.566

Alfa AF: 0.566 Hom.: 9412

Bravo AF: 0.585

Asia WGS AF: 0.721 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs679711; hg19: chr3-109529550;