1-1161712-G-A

Variant names:

• chr1-1161712-G-A
• rs1539635
• XR_007065350.1:n.2220G>A

Variant summary

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

The XR_007065350.1(LOC124903820):​n.2220G>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 0.548 in 151,898 control chromosomes in the GnomAD database, including 24,036 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 0.55 (24036 hom., cov: 32)
• Consequence: LOC124903820 XR_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 2 publications found

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83163 AN: 151780 Hom.: 24015 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.548 AC: 83213 AN: 151898 Hom.: 24036 Cov.: 32 AF XY: 0.547 AC XY: 40588 AN XY: 74262

African (AFR) AF: 0.372 AC: 15408 AN: 41432

American (AMR) AF: 0.704 AC: 10750 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2370 AN: 3466

East Asian (EAS) AF: 0.538 AC: 2759 AN: 5126

South Asian (SAS) AF: 0.587 AC: 2829 AN: 4816

European-Finnish (FIN) AF: 0.513 AC: 5418 AN: 10570

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41593 AN: 67890

Other (OTH) AF: 0.592 AC: 1251 AN: 2112

Alfa AF: 0.562 Hom.: 3072

Bravo AF: 0.555

Asia WGS AF: 0.585 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.76
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1539635; hg19: chr1-1097092;