rs2369304

Positions:

• chr14-95739733-G-A

Variant summary

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

The NR_148060.1(LOC107984703):​n.324-15512G>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 0.457 in 152,012 control chromosomes in the GnomAD database, including 18,767 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 0.46 (18767 hom., cov: 32)
• Consequence: LOC107984703 NR_148060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984703	NR_148060.1	n.324-15512G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000547644.6	n.251-15512G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000556386.1	n.327-15512G>A		intron_variant, non_coding_transcript_variant		1
	ENST00000553445.5	n.368-15512G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69401 AN: 151894 Hom.: 18720 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.457 AC: 69502 AN: 152012 Hom.: 18767 Cov.: 32 AF XY: 0.457 AC XY: 33964 AN XY: 74280

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.408

Alfa AF: 0.335 Hom.: 10678

Bravo AF: 0.464

Asia WGS AF: 0.382 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2369304; hg19: chr14-96206070;