rs1470123

Variant names:

• chr15-66697795-C-G
• rs1470123

Your query was ambiguous. Multiple possible variants found:

• chr15-66697795-C-G
• chr15-66697795-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.411 AC: 17054 AN: 41480

American (AMR) AF: 0.550 AC: 8407 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3472

East Asian (EAS) AF: 0.384 AC: 1985 AN: 5168

South Asian (SAS) AF: 0.471 AC: 2269 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3898 AN: 10554

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.450 AC: 30570 AN: 67976

Other (OTH) AF: 0.478 AC: 1007 AN: 2106

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1470123; hg19: chr15-66990133;