chr1-181309366-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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1020782;

hg19: chr1-181278502;

COSMIC: COSV59995138;