14-85753423-T-C

Position:

• chr14-85753423-T-C

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 0.973 in 152,202 control chromosomes in the GnomAD database, including 72,079 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 0.97 (72079 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.85753423T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.973 AC: 147969 AN: 152084 Hom.: 72028 Cov.: 31

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.986

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.973 AC: 148079 AN: 152202 Hom.: 72079 Cov.: 31 AF XY: 0.972 AC XY: 72281 AN XY: 74394

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.986

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.885

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.973

Alfa AF: 0.976 Hom.: 10267

Bravo AF: 0.974

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1957789; hg19: chr14-86219767;