rs41752

Variant names:

• chr7-116810801-A-G
• rs41752
• XR_007060489.1:n.-219A>G

Variant summary

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

The XR_007060489.1(LOC124901731):​n.-219A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,128 control chromosomes in the GnomAD database, including 10,368 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 0.34 (10368 hom., cov: 32)
• Consequence: LOC124901731 XR_007060489.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

Genes affected

LOC124901731 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901731	XR_007060489.1	n.-219A>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52432 AN: 152010 Hom.: 10380 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.344 AC: 52402 AN: 152128 Hom.: 10368 Cov.: 32 AF XY: 0.350 AC XY: 26004 AN XY: 74364

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.367

Alfa AF: 0.400 Hom.: 6442

Bravo AF: 0.336

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.84
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41752; hg19: chr7-116450855;