rs1953743

chr14-54185761-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_943883.3(LOC105370507):n.335-331G>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 0.482 in 152,004 control chromosomes in the GnomAD database, including 19,651 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 0.48 (19651 hom., cov: 32)
• Consequence: LOC105370507 XR_943883.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.856

Genes affected

LOC105370507 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370507	XR_943883.3	n.335-331G>A		intron_variant, non_coding_transcript_variant
LOC105370507	XR_001750980.2	n.335-331G>A		intron_variant, non_coding_transcript_variant
LOC105370507	XR_943882.3	n.335-331G>A		intron_variant, non_coding_transcript_variant
LOC105370507	XR_943884.2	n.335-331G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73197 AN: 151886 Hom.: 19652 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.482 AC: 73202 AN: 152004 Hom.: 19651 Cov.: 32 AF XY: 0.477 AC XY: 35459 AN XY: 74286

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.516

Alfa AF: 0.575 Hom.: 15658

Bravo AF: 0.463

Asia WGS AF: 0.385 AC: 1339 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
Cadd	Benign	21
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953743; hg19: chr14-54652479;