XR_001737977.2:n.106+5465T>C

Variant names:

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

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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 v4.9

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;