rs2498801

chr14-104769221-T-C

Variant summary

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

The XR_007064362.1(LOC102723342):n.3441T>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 0.406 in 196,072 control chromosomes in the GnomAD database, including 16,811 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 (13251 hom., cov: 33)
  • Exomes 𝑓: 0.39 (3560 hom.)
• Consequence: LOC102723342 XR_007064362.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

LOC102723342 (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 (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723342	XR_007064362.1	n.3441T>C		non_coding_transcript_exon_variant	2/2
LOC102723342	XR_007064363.1	n.1647T>C		non_coding_transcript_exon_variant	2/2
LOC102723342	XR_007064364.1	n.1263T>C		non_coding_transcript_exon_variant	3/3
LOC102723342	XR_429419.5	n.3057T>C		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62230 AN: 151904 Hom.: 13243 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.392 AC: 17259 AN: 44052 Hom.: 3560 AF XY: 0.390 AC XY: 8149 AN XY: 20912

Gnomad4 AFR exome AF: 0.456

Gnomad4 AMR exome AF: 0.484

Gnomad4 ASJ exome AF: 0.308

Gnomad4 EAS exome AF: 0.572

Gnomad4 SAS exome AF: 0.491

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.343

Gnomad4 OTH exome AF: 0.370

GnomAD4 genome AF: 0.410 AC: 62285 AN: 152020 Hom.: 13251 Cov.: 33 AF XY: 0.414 AC XY: 30755 AN XY: 74300

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.400

Alfa AF: 0.384 Hom.: 1407

Bravo AF: 0.418

Asia WGS AF: 0.589 AC: 2048 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	2.9
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2498801; hg19: chr14-105235558;