14-95714358-G-T

Position:

• chr14-95714358-G-T

Variant summary

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

The ENST00000547644.6(ENSG00000257275):​n.152+2460G>T 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 0.258 in 151,980 control chromosomes in the GnomAD database, including 5,625 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 0.26 (5625 hom., cov: 32)
• Consequence: ENST00000547644.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000547644.6	n.152+2460G>T		intron_variant, non_coding_transcript_variant		2
	ENST00000553445.5	n.269+2333G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39108 AN: 151862 Hom.: 5617 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.258 AC: 39156 AN: 151980 Hom.: 5625 Cov.: 32 AF XY: 0.257 AC XY: 19089 AN XY: 74306

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.226

Alfa AF: 0.213 Hom.: 4714

Bravo AF: 0.261

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2887399; hg19: chr14-96180695;