XR_001742606.2:n.503-62039C>T

Variant names:

• chr5-13458257-G-A
• rs1373992
• XR_001742606.2:n.503-62039C>T

Variant summary

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

The XR_001742606.2(LOC105374660):​n.503-62039C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,856 control chromosomes in the GnomAD database, including 3,033 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 0.19 (3033 hom., cov: 32)
• Consequence: LOC105374660 XR_001742606.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 5 publications found

Genes affected

LOC105374660 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374660	XR_001742606.2	n.503-62039C>T		intron_variant	Intron 3 of 3
LOC105374660	XR_007058696.1	n.766+58078C>T		intron_variant	Intron 4 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29119 AN: 151738 Hom.: 3028 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.192 AC: 29130 AN: 151856 Hom.: 3033 Cov.: 32 AF XY: 0.198 AC XY: 14662 AN XY: 74212

African (AFR) AF: 0.159 AC: 6566 AN: 41422

American (AMR) AF: 0.216 AC: 3292 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1834 AN: 5120

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4812

European-Finnish (FIN) AF: 0.229 AC: 2413 AN: 10534

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12583 AN: 67916

Other (OTH) AF: 0.198 AC: 417 AN: 2106

Alfa AF: 0.190 Hom.: 7735

Bravo AF: 0.193

Asia WGS AF: 0.314 AC: 1092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.52
PhyloP100		-0.061

Splicing

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

Other links and lift over

dbSNP: rs1373992; hg19: chr5-13458367; COSMIC: COSV66933287;