XR_001738525.2:n.2381A>G

Variant names:

• chr1-232948998-T-C
• rs3820124
• XR_001738525.2:n.2381A>G

Variant summary

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

The XR_001738525.2(LOC107985361):​n.2381A>G 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 0.243 in 152,126 control chromosomes in the GnomAD database, including 4,589 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 0.24 (4589 hom., cov: 32)
• Consequence: LOC107985361 XR_001738525.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 16 publications found

Genes affected

LOC107985361 (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 (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795688.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303568	ENST00000795688.1		n.255-649A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36900 AN: 152008 Hom.: 4569 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.243 AC: 36966 AN: 152126 Hom.: 4589 Cov.: 32 AF XY: 0.240 AC XY: 17837 AN XY: 74350

African (AFR) AF: 0.307 AC: 12741 AN: 41462

American (AMR) AF: 0.183 AC: 2794 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1064 AN: 5184

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4824

European-Finnish (FIN) AF: 0.186 AC: 1966 AN: 10580

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15573 AN: 68000

Other (OTH) AF: 0.246 AC: 520 AN: 2112

Alfa AF: 0.236 Hom.: 13642

Bravo AF: 0.245

Asia WGS AF: 0.240 AC: 836 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	0.68
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3820124; hg19: chr1-233084744;