chr1-58765488-A-G

Variant names:

• chr1-58765488-A-G
• rs1007271
• XR_007066136.1:n.4476A>G

Variant summary

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

The XR_007066136.1(LOC105378751):​n.4476A>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 0.568 in 152,076 control chromosomes in the GnomAD database, including 27,678 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 0.57 (27678 hom., cov: 32)
• Consequence: LOC105378751 XR_007066136.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 7 publications found

Genes affected

LOC105378751 (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 (AMR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378751	XR_007066136.1	n.4476A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105378751	XR_007066137.1	n.4476A>G		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283445	ENST00000636386.1	n.330-622A>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86282 AN: 151958 Hom.: 27660 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.568 AC: 86313 AN: 152076 Hom.: 27678 Cov.: 32 AF XY: 0.573 AC XY: 42586 AN XY: 74334

African (AFR) AF: 0.238 AC: 9885 AN: 41488

American (AMR) AF: 0.695 AC: 10628 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2390 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3156 AN: 5172

South Asian (SAS) AF: 0.665 AC: 3205 AN: 4816

European-Finnish (FIN) AF: 0.726 AC: 7657 AN: 10552

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47190 AN: 67978

Other (OTH) AF: 0.591 AC: 1247 AN: 2110

Alfa AF: 0.645 Hom.: 89240

Bravo AF: 0.552

Asia WGS AF: 0.614 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs1007271; hg19: chr1-59231160;