14-36585106-C-T

Position:

• chr14-36585106-C-T

Variant summary

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

The ENST00000634305.1(ENSG00000283098):​n.323-69643C>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 0.0622 in 152,304 control chromosomes in the GnomAD database, including 864 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 0.062 (864 hom., cov: 33)
• Consequence: ENST00000634305.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 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
	ENST00000634305.1	n.323-69643C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9455 AN: 152186 Hom.: 861 Cov.: 33

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0267

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0230

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.0473

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

GnomAD4 genome AF: 0.0622 AC: 9474 AN: 152304 Hom.: 864 Cov.: 33 AF XY: 0.0607 AC XY: 4521 AN XY: 74476

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.0266

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0224

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00304

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0156 Hom.: 215

Bravo AF: 0.0707

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	22
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs177322; hg19: chr14-37054311;