14-36571123-T-G

Position:

• chr14-36571123-T-G

Variant summary

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

The ENST00000634305.1(ENSG00000283098):​n.323-83626T>G 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 0.67 in 152,078 control chromosomes in the GnomAD database, including 35,058 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 0.67 (35058 hom., cov: 33)
• Consequence: ENST00000634305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370453	XR_001750715.2	n.703-1054T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634305.1	n.323-83626T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.670 AC: 101792 AN: 151960 Hom.: 35036 Cov.: 33

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.670 AC: 101858 AN: 152078 Hom.: 35058 Cov.: 33 AF XY: 0.660 AC XY: 49075 AN XY: 74342

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.690

Alfa AF: 0.748 Hom.: 82609

Bravo AF: 0.662

Asia WGS AF: 0.502 AC: 1749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs427490; hg19: chr14-37040328;