14-20879073-C-T

Position:

• chr14-20879073-C-T

Variant summary

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

The XR_110261.4(LOC100507513):​n.723-3330G>A 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 0.622 in 152,114 control chromosomes in the GnomAD database, including 32,520 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 0.62 (32520 hom., cov: 32)
• Consequence: LOC100507513 XR_110261.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

LOC100507513 (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 (AMR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100507513	XR_110261.4	n.723-3330G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94552 AN: 151996 Hom.: 32505 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.622 AC: 94605 AN: 152114 Hom.: 32520 Cov.: 32 AF XY: 0.628 AC XY: 46675 AN XY: 74352

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.652

Alfa AF: 0.684 Hom.: 4709

Bravo AF: 0.608

Asia WGS AF: 0.677 AC: 2354 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	2.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11156734; hg19: chr14-21347232;