5-13502954-T-G

Variant names:

• chr5-13502954-T-G
• rs3868287
• XR_001742606.2:n.502+73638A>C

Variant summary

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

The XR_001742606.2(LOC105374660):​n.502+73638A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,084 control chromosomes in the GnomAD database, including 4,882 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 0.23 (4882 hom., cov: 32)
• Consequence: LOC105374660 XR_001742606.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.283 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: 0.232 AC: 35324 AN: 151966 Hom.: 4880 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.232 AC: 35314 AN: 152084 Hom.: 4882 Cov.: 32 AF XY: 0.237 AC XY: 17639 AN XY: 74324

African (AFR) AF: 0.0899 AC: 3733 AN: 41528

American (AMR) AF: 0.268 AC: 4093 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3466

East Asian (EAS) AF: 0.267 AC: 1384 AN: 5178

South Asian (SAS) AF: 0.158 AC: 761 AN: 4808

European-Finnish (FIN) AF: 0.387 AC: 4082 AN: 10544

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.286 AC: 19433 AN: 67966

Other (OTH) AF: 0.252 AC: 532 AN: 2108

Alfa AF: 0.245 Hom.: 3463

Bravo AF: 0.219

Asia WGS AF: 0.174 AC: 606 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	8.1
DANN	Benign	0.74
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs3868287; hg19: chr5-13503064;