rs1470123

chr15-66697795-C-Gchr15-66697795-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 0.442 in 152,060 control chromosomes in the GnomAD database, including 14,998 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 0.44 (14998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67117 AN: 151942 Hom.: 14996 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.442 AC: 67153 AN: 152060 Hom.: 14998 Cov.: 32 AF XY: 0.442 AC XY: 32833 AN XY: 74330

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.478

Alfa AF: 0.443 Hom.: 1861

Bravo AF: 0.454

Asia WGS AF: 0.414 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.5
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1470123; hg19: chr15-66990133;