rs41303970

Positions:

• chr1-93909753-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007066230.1(LOC124904221):​n.162G>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: LOC124904221 XR_007066230.1 non_coding_transcript_exon
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 0.337

Genes affected

LOC124904221 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124904221	XR_007066230.1	n.162G>A		non_coding_transcript_exon_variant	1/2
		n.93909753G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.193

Alfa AF: 0.178 Hom.: 325

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

risk factor, no assertion criteria provided

literature only

OMIM

Sep 23, 2003

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41303970; hg19: chr1-94375309;