rs1539636

chr1-1161528-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007065351.1(LOC124903820):n.1318T>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_007065351.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124903820	XR_007065351.1	n.1318T>C		non_coding_transcript_exon_variant	3/3
LOC124903820	XR_007065350.1	n.2036T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.875

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.862

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539636; hg19: chr1-1096908;