rs12728740

Variant names:

• chr1-159740303-C-A
• rs12728740

Your query was ambiguous. Multiple possible variants found:

• chr1-159740303-C-A
• chr1-159740303-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 0.261 in 152,118 control chromosomes in the GnomAD database, including 6,531 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 0.26 (6531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.338 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: 0.261 AC: 39634 AN: 152000 Hom.: 6530 Cov.: 32

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.261 AC: 39648 AN: 152118 Hom.: 6531 Cov.: 32 AF XY: 0.267 AC XY: 19867 AN XY: 74340

Gnomad4 AFR AF: 0.0686

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.265

Alfa AF: 0.316 Hom.: 7338

Bravo AF: 0.244

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12728740; hg19: chr1-159710093;