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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986406	XR_001742607.2	n.1366-4136C>T		intron_variant	Intron 1 of 1
LOC107986406	XR_001742608.2	n.1366-4136C>T		intron_variant	Intron 1 of 2
LOC107986406	XR_001742610.1	n.533-4136C>T		intron_variant	Intron 1 of 3

Ensembl

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

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 v4.3

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;