rs1961472

Variant names:

• chr5-15973329-C-T
• rs1961472
• XR_001742607.2:n.1366-4136C>T

Variant summary

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

The XR_001742607.2(LOC107986406):​n.1366-4136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,144 control chromosomes in the GnomAD database, including 1,581 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 0.085 (1581 hom., cov: 33)
• Consequence: LOC107986406 XR_001742607.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 1 publications found

Genes affected

LOC107986406 (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 = 0.269 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12853 AN: 152026 Hom.: 1579 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.00913

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00922

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0847 AC: 12892 AN: 152144 Hom.: 1581 Cov.: 33 AF XY: 0.0826 AC XY: 6145 AN XY: 74388

African (AFR) AF: 0.273 AC: 11318 AN: 41450

American (AMR) AF: 0.0457 AC: 699 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00403 AC: 14 AN: 3470

East Asian (EAS) AF: 0.00406 AC: 21 AN: 5178

South Asian (SAS) AF: 0.00935 AC: 45 AN: 4814

European-Finnish (FIN) AF: 0.00123 AC: 13 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00922 AC: 627 AN: 68020

Other (OTH) AF: 0.0649 AC: 137 AN: 2110

Alfa AF: 0.0434 Hom.: 358

Bravo AF: 0.0965

Asia WGS AF: 0.0200 AC: 70 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.57
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1961472; hg19: chr5-15973438;