chr14-65178532-T-C

Variant names:

• chr14-65178532-T-C
• rs7158173

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 0.471 in 151,962 control chromosomes in the GnomAD database, including 18,050 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 0.47 (18050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

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 (AMR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71576 AN: 151844 Hom.: 18051 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.471 AC: 71597 AN: 151962 Hom.: 18050 Cov.: 32 AF XY: 0.473 AC XY: 35160 AN XY: 74270

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.486

Alfa AF: 0.528 Hom.: 32100

Bravo AF: 0.471

Asia WGS AF: 0.431 AC: 1497 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	0.29
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7158173; hg19: chr14-65645250;