5-171797539-A-T

Variant names:

• chr5-171797539-A-T
• rs254962
• XR_001742985.3:n.3056-1803T>A

Variant summary

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

The XR_001742985.3(LOC105377725):​n.3056-1803T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 152,294 control chromosomes in the GnomAD database, including 1,684 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 0.092 (1684 hom., cov: 33)
• Consequence: LOC105377725 XR_001742985.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 1 publications found

Genes affected

LOC105377725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0920 AC: 13999 AN: 152174 Hom.: 1665 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0117

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0923 AC: 14050 AN: 152294 Hom.: 1684 Cov.: 33 AF XY: 0.0905 AC XY: 6739 AN XY: 74504

African (AFR) AF: 0.286 AC: 11880 AN: 41510

American (AMR) AF: 0.0446 AC: 682 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.0152 AC: 79 AN: 5192

South Asian (SAS) AF: 0.0501 AC: 242 AN: 4830

European-Finnish (FIN) AF: 0.0151 AC: 160 AN: 10630

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0117 AC: 798 AN: 68042

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.0168 Hom.: 30

Bravo AF: 0.102

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.89
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs254962; hg19: chr5-171224543;