rs12728740

Variant names:

• chr1-159740303-C-A
• rs12728740
• ENST00000751816.1:n.*39C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-159740303-C-A
• chr1-159740303-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751816.1(ENSG00000297913):​n.*39C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297913 ENST00000751816.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 4 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297913	ENST00000751816.1		n.*39C>A		downstream_gene	N/A
	ENSG00000297913	ENST00000751817.1		n.*216C>A		downstream_gene	N/A
	ENSG00000297913	ENST00000751818.1		n.*214C>A		downstream_gene	N/A

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

African (AFR) AF: 0.0686 AC: 2848 AN: 41538

American (AMR) AF: 0.332 AC: 5076 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.0582 AC: 301 AN: 5176

South Asian (SAS) AF: 0.282 AC: 1363 AN: 4828

European-Finnish (FIN) AF: 0.459 AC: 4835 AN: 10544

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23219 AN: 67972

Other (OTH) AF: 0.265 AC: 560 AN: 2112

Alfa AF: 0.309 Hom.: 9485

Bravo AF: 0.244

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12728740;

hg19: chr1-159710093;