7-150562311-A-G

Variant names:

• chr7-150562311-A-G
• rs2140138
• XM_017012936.2:c.571+902T>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+902T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,088 control chromosomes in the GnomAD database, including 10,830 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 (10830 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 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: 0.340 AC: 51634 AN: 151970 Hom.: 10796 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.340 AC: 51723 AN: 152088 Hom.: 10830 Cov.: 32 AF XY: 0.342 AC XY: 25449 AN XY: 74344

African (AFR) AF: 0.596 AC: 24688 AN: 41448

American (AMR) AF: 0.263 AC: 4022 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 831 AN: 3468

East Asian (EAS) AF: 0.363 AC: 1881 AN: 5176

South Asian (SAS) AF: 0.385 AC: 1852 AN: 4816

European-Finnish (FIN) AF: 0.238 AC: 2521 AN: 10590

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15010 AN: 67992

Other (OTH) AF: 0.302 AC: 639 AN: 2116

Alfa AF: 0.285 Hom.: 1584

Bravo AF: 0.350

Asia WGS AF: 0.380 AC: 1318 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.39
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2140138; hg19: chr7-150259399;