rs4508366

chr14-94600900-T-Cchr14-94600900-T-G

Variant summary

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

The ENST00000656621.1(ENSG00000288028):n.70+1371T>C 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 0.386 in 151,290 control chromosomes in the GnomAD database, including 12,412 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 0.39 (12412 hom., cov: 31)
• Consequence: ENST00000656621.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

(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 (AFR) allele frequency at 95% confidence interval = 0.578 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
	ENST00000656621.1	n.70+1371T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58325 AN: 151172 Hom.: 12386 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.386 AC: 58393 AN: 151290 Hom.: 12412 Cov.: 31 AF XY: 0.380 AC XY: 28103 AN XY: 73894

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.366

Alfa AF: 0.365 Hom.: 1377

Bravo AF: 0.391

Asia WGS AF: 0.340 AC: 1184 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	1.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4508366; hg19: chr14-95067237;