chr14-48909045-C-T

Position:

• chr14-48909045-C-T

Variant summary

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

The variant allele was found at a frequency of 0.291 in 151,950 control chromosomes in the GnomAD database, including 6,720 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 0.29 (6720 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.48909045C>T		intergenic_region
LOC105378178	XR_007064152.1	n.345+160747G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44153 AN: 151832 Hom.: 6714 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.291 AC: 44174 AN: 151950 Hom.: 6720 Cov.: 32 AF XY: 0.291 AC XY: 21627 AN XY: 74256

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.302

Alfa AF: 0.267 Hom.: 10825

Bravo AF: 0.287

Asia WGS AF: 0.237 AC: 822 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1986410; hg19: chr14-49378248;