rs1539635

Positions:

• chr1-1161712-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124903820 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.2220G>A		non_coding_transcript_exon_variant	2/2
LOC124903820	XR_007065351.1	n.1502G>A		non_coding_transcript_exon_variant	3/3
		n.1161712G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.613

Gnomad4 OTH AF: 0.592

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1539635; hg19: chr1-1097092;