3-856978-C-T

Position:

• chr3-856978-C-T

Variant summary

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

The XR_001740584.1(LOC107986058):​n.1837C>T 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 0.362 in 151,832 control chromosomes in the GnomAD database, including 10,169 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 0.36 (10169 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LOC107986058 XR_001740584.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LOC107986058 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986058	XR_001740584.1	n.1837C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54972 AN: 151710 Hom.: 10175 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.378

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.362 AC: 54988 AN: 151828 Hom.: 10169 Cov.: 33 AF XY: 0.366 AC XY: 27141 AN XY: 74180

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.382

Alfa AF: 0.364 Hom.: 8963

Bravo AF: 0.361

Asia WGS AF: 0.504 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35964523; hg19: chr3-898661;