XR_007060588.1:n.699-4996A>G

Variant names:

• chr7-150653887-T-C
• rs10256482
• XR_007060588.1:n.699-4996A>G

Variant summary

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

The XR_007060588.1(LOC124901774):​n.699-4996A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,890 control chromosomes in the GnomAD database, including 17,245 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 0.47 (17245 hom., cov: 31)
• Consequence: LOC124901774 XR_007060588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 9 publications found

Genes affected

LOC124901774 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 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: 0.471 AC: 71445 AN: 151772 Hom.: 17225 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.471 AC: 71513 AN: 151890 Hom.: 17245 Cov.: 31 AF XY: 0.477 AC XY: 35414 AN XY: 74196

African (AFR) AF: 0.541 AC: 22384 AN: 41400

American (AMR) AF: 0.499 AC: 7627 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2550 AN: 5142

South Asian (SAS) AF: 0.548 AC: 2637 AN: 4814

European-Finnish (FIN) AF: 0.503 AC: 5311 AN: 10552

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27989 AN: 67926

Other (OTH) AF: 0.432 AC: 911 AN: 2108

Alfa AF: 0.433 Hom.: 28171

Bravo AF: 0.474

Asia WGS AF: 0.516 AC: 1793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10256482; hg19: chr7-150350975;