rs171740

Variant names:

• chr5-53714127-A-G
• rs171740
• XR_007058768.1:n.515+705A>G

Variant summary

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

The XR_007058768.1(LOC124900975):​n.515+705A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,124 control chromosomes in the GnomAD database, including 6,173 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 0.25 (6173 hom., cov: 32)
• Consequence: LOC124900975 XR_007058768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

Genes affected

LOC124900975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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: 0.250 AC: 37944 AN: 152006 Hom.: 6156 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.250 AC: 38000 AN: 152124 Hom.: 6173 Cov.: 32 AF XY: 0.251 AC XY: 18638 AN XY: 74374

African (AFR) AF: 0.449 AC: 18604 AN: 41468

American (AMR) AF: 0.213 AC: 3257 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 630 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2394 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1265 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1430 AN: 10616

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9771 AN: 67980

Other (OTH) AF: 0.255 AC: 539 AN: 2116

Alfa AF: 0.210 Hom.: 600

Bravo AF: 0.266

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.3
DANN	Benign	0.78
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs171740; hg19: chr5-53009957;