rs10256482

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901774	XR_007060588.1	n.699-4996A>G		intron_variant	Intron 2 of 2
LOC124901774	XR_007060589.1	n.285-4996A>G		intron_variant	Intron 3 of 3

Ensembl

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

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 v4.3

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;