rs4727157

chr7-88313734-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060420.1(LOC124901692):n.825-19027G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

Genes affected

LOC124901692 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901692	XR_007060420.1	n.825-19027G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0202

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0527

Gnomad4 OTH AF: 0.0562

Alfa AF: 0.0534 Hom.: 105

Bravo AF: 0.0454

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.1
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4727157; hg19: chr7-87943049;