rs12744244

Variant names:

• chr1-159677866-C-A
• rs12744244
• ENST00000751816.1:n.107+17177C>A

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+17177C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,222 control chromosomes in the GnomAD database, including 2,032 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 0.14 (2032 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 11 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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.107+17177C>A		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.109+17177C>A		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.62+17177C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21815 AN: 152104 Hom.: 2032 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0552

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.143 AC: 21820 AN: 152222 Hom.: 2032 Cov.: 32 AF XY: 0.141 AC XY: 10512 AN XY: 74428

African (AFR) AF: 0.0375 AC: 1560 AN: 41556

American (AMR) AF: 0.139 AC: 2128 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3470

East Asian (EAS) AF: 0.000964 AC: 5 AN: 5188

South Asian (SAS) AF: 0.0561 AC: 271 AN: 4832

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14369 AN: 67984

Other (OTH) AF: 0.162 AC: 342 AN: 2112

Alfa AF: 0.161 Hom.: 1442

Bravo AF: 0.136

Asia WGS AF: 0.0380 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.79
PhyloP100		0.23

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: rs12744244;

hg19: chr1-159647656;