rs589249

Variant names:

• chr1-36696751-A-G
• rs589249
• XR_001737977.2:n.106+5465T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-36696751-A-G
• chr1-36696751-A-T

Variant summary

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

The XR_001737977.2(LOC107984941):​n.106+5465T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,104 control chromosomes in the GnomAD database, including 21,612 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 0.49 (21612 hom., cov: 32)
• Consequence: LOC107984941 XR_001737977.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 15 publications found

Genes affected

LOC107984941 (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 (AFR) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984941	XR_001737977.2	n.106+5465T>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74063 AN: 151986 Hom.: 21563 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.488 AC: 74164 AN: 152104 Hom.: 21612 Cov.: 32 AF XY: 0.488 AC XY: 36239 AN XY: 74336

African (AFR) AF: 0.814 AC: 33777 AN: 41508

American (AMR) AF: 0.495 AC: 7573 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2888 AN: 5152

South Asian (SAS) AF: 0.440 AC: 2119 AN: 4816

European-Finnish (FIN) AF: 0.348 AC: 3680 AN: 10576

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21861 AN: 67964

Other (OTH) AF: 0.473 AC: 1000 AN: 2114

Alfa AF: 0.412 Hom.: 12668

Bravo AF: 0.515

Asia WGS AF: 0.561 AC: 1954 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	7.1
DANN	Benign	0.77
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs589249; hg19: chr1-37162352;