rs10486156

Variant names:

• chr7-7309002-C-T
• rs10486156
• XR_002956539.2:n.441+37158C>T

Variant summary

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

The XR_002956539.2(LOC107986764):​n.441+37158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,096 control chromosomes in the GnomAD database, including 5,481 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 0.25 (5481 hom., cov: 32)
• Consequence: LOC107986764 XR_002956539.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 6 publications found

Genes affected

LOC107986764 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38086 AN: 151976 Hom.: 5478 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.251 AC: 38107 AN: 152096 Hom.: 5481 Cov.: 32 AF XY: 0.254 AC XY: 18863 AN XY: 74370

African (AFR) AF: 0.108 AC: 4470 AN: 41488

American (AMR) AF: 0.333 AC: 5091 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1576 AN: 5166

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4808

European-Finnish (FIN) AF: 0.289 AC: 3059 AN: 10570

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20916 AN: 67992

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.287 Hom.: 11338

Bravo AF: 0.246

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.27
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10486156; hg19: chr7-7348633;