rs4727157

Variant names:

• chr7-88313734-G-A
• rs4727157
• XR_007060420.1:n.825-19027G>A

Variant summary

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

The XR_007060420.1(LOC124901692):​n.825-19027G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0452 in 152,244 control chromosomes in the GnomAD database, including 175 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 0.045 (175 hom., cov: 32)
• Consequence: LOC124901692 XR_007060420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 2 publications found

Genes affected

LOC124901692 (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 = 0.0806 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: 0.0454 AC: 6900 AN: 152126 Hom.: 176 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0589

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0452 AC: 6889 AN: 152244 Hom.: 175 Cov.: 32 AF XY: 0.0461 AC XY: 3430 AN XY: 74436

African (AFR) AF: 0.0202 AC: 840 AN: 41534

American (AMR) AF: 0.0632 AC: 966 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3468

East Asian (EAS) AF: 0.0583 AC: 302 AN: 5184

South Asian (SAS) AF: 0.0875 AC: 422 AN: 4822

European-Finnish (FIN) AF: 0.0376 AC: 398 AN: 10596

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0527 AC: 3584 AN: 68026

Other (OTH) AF: 0.0562 AC: 119 AN: 2116

Alfa AF: 0.0530 Hom.: 113

Bravo AF: 0.0454

Asia WGS AF: 0.0590 AC: 206 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	1.1
DANN	Benign	0.58
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs4727157; hg19: chr7-87943049;