7-150562476-A-G

Variant names:

• chr7-150562476-A-G
• rs12531207
• XM_017012936.2:c.571+737T>C

Variant summary

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

The XM_017012936.2(LOC107986860):​c.571+737T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,068 control chromosomes in the GnomAD database, including 10,304 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 0.36 (10304 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 3 publications found

Genes affected

LOC107986860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 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: 0.356 AC: 54052 AN: 151950 Hom.: 10307 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.356 AC: 54063 AN: 152068 Hom.: 10304 Cov.: 32 AF XY: 0.361 AC XY: 26822 AN XY: 74314

African (AFR) AF: 0.230 AC: 9550 AN: 41504

American (AMR) AF: 0.405 AC: 6183 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3468

East Asian (EAS) AF: 0.380 AC: 1964 AN: 5170

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4822

European-Finnish (FIN) AF: 0.529 AC: 5578 AN: 10538

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26598 AN: 67972

Other (OTH) AF: 0.341 AC: 721 AN: 2112

Alfa AF: 0.376 Hom.: 1834

Bravo AF: 0.342

Asia WGS AF: 0.388 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	7.4
DANN	Benign	0.93
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12531207; hg19: chr7-150259564;