rs41303970

Variant names:

• chr1-93909753-G-A
• rs41303970
• ENST00000789326.1:n.80G>A

Variant summary

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

The ENST00000789326.1(ENSG00000302751):​n.80G>A 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 0.186 in 151,700 control chromosomes in the GnomAD database, including 2,800 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.19 (2800 hom., cov: 32)
• Consequence: ENSG00000302751 ENST00000789326.1 non_coding_transcript_exon
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 0.337
• Publications: 34 publications found

Genes affected

ENSG00000302751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904221	XR_007066230.1	n.162G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302751	ENST00000789326.1	n.80G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000302751	ENST00000789327.1	n.-17G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28203 AN: 151590 Hom.: 2792 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0925

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.186 AC: 28235 AN: 151700 Hom.: 2800 Cov.: 32 AF XY: 0.186 AC XY: 13760 AN XY: 74174

African (AFR) AF: 0.208 AC: 8567 AN: 41206

American (AMR) AF: 0.298 AC: 4547 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3468

East Asian (EAS) AF: 0.162 AC: 832 AN: 5122

South Asian (SAS) AF: 0.0923 AC: 445 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1297 AN: 10570

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11402 AN: 67922

Other (OTH) AF: 0.193 AC: 408 AN: 2112

Alfa AF: 0.189 Hom.: 589

Bravo AF: 0.204

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Myocardial infarction, susceptibility to Other:1

Sep 23, 2003

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.70
PhyloP100		0.34
PromoterAI		0.058	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41303970; hg19: chr1-94375309;