chr1-15753676-G-A

Variant names:

• chr1-15753676-G-A
• rs12725198
• ENST00000746726.1:n.1116C>T

Variant summary

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

The ENST00000746726.1(ENSG00000297277):​n.1116C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,170 control chromosomes in the GnomAD database, including 3,345 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 0.21 (3345 hom., cov: 32)
• Consequence: ENSG00000297277 ENST00000746726.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 17 publications found

Genes affected

ENSG00000297277 (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 (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746726.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297277	ENST00000746726.1		n.1116C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31270 AN: 152052 Hom.: 3343 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0709

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.205 AC: 31267 AN: 152170 Hom.: 3345 Cov.: 32 AF XY: 0.200 AC XY: 14893 AN XY: 74384

African (AFR) AF: 0.214 AC: 8882 AN: 41532

American (AMR) AF: 0.153 AC: 2341 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5176

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4816

European-Finnish (FIN) AF: 0.148 AC: 1569 AN: 10600

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15371 AN: 67988

Other (OTH) AF: 0.204 AC: 430 AN: 2110

Alfa AF: 0.220 Hom.: 17202

Bravo AF: 0.204

Asia WGS AF: 0.148 AC: 514 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	0.20
DANN	Benign	0.58
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs12725198; hg19: chr1-16080171;