chr14-53623359-T-G

Position:

• chr14-53623359-T-G

Variant summary

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

The ENST00000648066.1(ENSG00000237356):​n.335-63840T>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 0.161 in 152,188 control chromosomes in the GnomAD database, including 2,143 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 0.16 (2143 hom., cov: 32)
• Consequence: ENST00000648066.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370504	XR_943876.3	n.29701-63840T>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750974.1	n.3896-63840T>G		intron_variant, non_coding_transcript_variant
LOC105370504	XR_001750975.3	n.29701-63840T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648066.1	n.335-63840T>G		intron_variant, non_coding_transcript_variant
	ENST00000456100.6	n.326-63840T>G		intron_variant, non_coding_transcript_variant		4
	ENST00000663444.1	n.560-63840T>G		intron_variant, non_coding_transcript_variant
	ENST00000669612.1	n.398-63840T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24518 AN: 152070 Hom.: 2142 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.161 AC: 24525 AN: 152188 Hom.: 2143 Cov.: 32 AF XY: 0.158 AC XY: 11754 AN XY: 74416

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0793

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.180

Alfa AF: 0.195 Hom.: 1444

Bravo AF: 0.156

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.95
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10483623; hg19: chr14-54090077;