chr5-113937501-G-T

Variant names:

• chr5-113937501-G-T
• rs1905155
• XR_007058906.1:n.2086-60675G>T

Variant summary

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

The XR_007058906.1(LOC124901047):​n.2086-60675G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,008 control chromosomes in the GnomAD database, including 2,784 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 0.18 (2784 hom., cov: 32)
• Consequence: LOC124901047 XR_007058906.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 1 publications found

Genes affected

LOC124901047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 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: 0.182 AC: 27585 AN: 151890 Hom.: 2785 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.181 AC: 27587 AN: 152008 Hom.: 2784 Cov.: 32 AF XY: 0.186 AC XY: 13814 AN XY: 74286

African (AFR) AF: 0.102 AC: 4224 AN: 41468

American (AMR) AF: 0.171 AC: 2612 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3470

East Asian (EAS) AF: 0.141 AC: 730 AN: 5166

South Asian (SAS) AF: 0.227 AC: 1090 AN: 4808

European-Finnish (FIN) AF: 0.297 AC: 3131 AN: 10540

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14529 AN: 67980

Other (OTH) AF: 0.163 AC: 342 AN: 2102

Alfa AF: 0.202 Hom.: 1742

Bravo AF: 0.168

Asia WGS AF: 0.186 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1905155; hg19: chr5-113273198; COSMIC: COSV60184114;