rs1539635

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903820	XR_007065350.1	n.2220G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124903820	XR_007065351.1	n.1502G>A		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: 0.548 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 v4.3

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;