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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.2036T>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124903820	XR_007065351.1	n.1318T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

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

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 v4.3

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;