7-150715203-C-G

Variant names:

• chr7-150715203-C-G
• rs1558479

Variant summary

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

The variant allele was found at a frequency of 0.322 in 152,020 control chromosomes in the GnomAD database, including 8,079 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 0.32 (8079 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.746
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.322 AC: 48934 AN: 151902 Hom.: 8061 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.322 AC: 49004 AN: 152020 Hom.: 8079 Cov.: 31 AF XY: 0.326 AC XY: 24194 AN XY: 74312

African (AFR) AF: 0.302 AC: 12504 AN: 41454

American (AMR) AF: 0.324 AC: 4943 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1244 AN: 3472

East Asian (EAS) AF: 0.487 AC: 2521 AN: 5178

South Asian (SAS) AF: 0.303 AC: 1461 AN: 4824

European-Finnish (FIN) AF: 0.352 AC: 3713 AN: 10558

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21523 AN: 67938

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.182 Hom.: 374

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.59
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs1558479; hg19: chr7-150412291;