1-181309366-T-G

Variant names:

• chr1-181309366-T-G
• rs1020782
• XR_001737809.1:n.154T>G

Variant summary

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

The XR_001737809.1(LOC107985454):​n.154T>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 0.592 in 152,090 control chromosomes in the GnomAD database, including 26,903 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 0.59 (26903 hom., cov: 33)
• Consequence: LOC107985454 XR_001737809.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 2 publications found

Genes affected

LOC107985454 (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 (EAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985454	XR_001737809.1	n.154T>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89945 AN: 151972 Hom.: 26877 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.592 AC: 90020 AN: 152090 Hom.: 26903 Cov.: 33 AF XY: 0.596 AC XY: 44291 AN XY: 74344

African (AFR) AF: 0.637 AC: 26436 AN: 41470

American (AMR) AF: 0.612 AC: 9358 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1656 AN: 3472

East Asian (EAS) AF: 0.793 AC: 4109 AN: 5184

South Asian (SAS) AF: 0.644 AC: 3099 AN: 4812

European-Finnish (FIN) AF: 0.576 AC: 6091 AN: 10574

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37388 AN: 67982

Other (OTH) AF: 0.573 AC: 1210 AN: 2110

Alfa AF: 0.590 Hom.: 3896

Bravo AF: 0.598

Asia WGS AF: 0.684 AC: 2375 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	2.8
DANN	Benign	0.70
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1020782; hg19: chr1-181278502; COSMIC: COSV59995138;