rs1539636

Variant names:

• chr1-1161528-T-C
• rs1539636
• XR_007065350.1:n.2036T>C

Variant summary

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

The XR_007065350.1(LOC124903820):​n.2036T>C 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 0.876 in 152,282 control chromosomes in the GnomAD database, including 58,838 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 0.88 (58838 hom., cov: 35)
• Consequence: LOC124903820 XR_007065350.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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: 0.876 AC: 133231 AN: 152164 Hom.: 58792 Cov.: 35

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.876 AC: 133335 AN: 152282 Hom.: 58838 Cov.: 35 AF XY: 0.874 AC XY: 65079 AN XY: 74458

African (AFR) AF: 0.817 AC: 33928 AN: 41542

American (AMR) AF: 0.889 AC: 13611 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3100 AN: 3472

East Asian (EAS) AF: 0.596 AC: 3078 AN: 5166

South Asian (SAS) AF: 0.875 AC: 4229 AN: 4832

European-Finnish (FIN) AF: 0.900 AC: 9554 AN: 10612

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62862 AN: 68032

Other (OTH) AF: 0.862 AC: 1823 AN: 2116

Alfa AF: 0.895 Hom.: 7580

Bravo AF: 0.869

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.50
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1539636; hg19: chr1-1096908;