rs12743074

Variant names:

• chr1-248768834-C-T
• rs12743074
• ENST00000825170.1:n.250-11516C>T

Variant summary

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

The ENST00000825170.1(ENSG00000293517):​n.250-11516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,114 control chromosomes in the GnomAD database, including 1,939 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 0.13 (1939 hom., cov: 32)
• Consequence: ENSG00000293517 ENST00000825170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 1 publications found

Genes affected

ENSG00000293517 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825170.1. 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
	ENSG00000293517	ENST00000825170.1		n.250-11516C>T		intron	N/A
	ENSG00000293517	ENST00000825203.1		n.266+28730C>T		intron	N/A
	ENSG00000293517	ENST00000825204.1		n.260+28730C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20251 AN: 151996 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.133 AC: 20281 AN: 152114 Hom.: 1939 Cov.: 32 AF XY: 0.129 AC XY: 9571 AN XY: 74362

African (AFR) AF: 0.254 AC: 10545 AN: 41472

American (AMR) AF: 0.0643 AC: 982 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 340 AN: 3462

East Asian (EAS) AF: 0.209 AC: 1078 AN: 5170

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4816

European-Finnish (FIN) AF: 0.0506 AC: 536 AN: 10598

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0917 AC: 6233 AN: 68002

Other (OTH) AF: 0.107 AC: 227 AN: 2114

Alfa AF: 0.121 Hom.: 189

Bravo AF: 0.140

Asia WGS AF: 0.135 AC: 469 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.48
PhyloP100		0.19

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: rs12743074;

hg19: chr1-249063033;