rs7547997

Variant names:

• chr1-158371483-G-A
• rs7547997

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 0.291 in 152,014 control chromosomes in the GnomAD database, including 9,382 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 0.29 (9382 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• Publications: 8 publications found

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 = 0.593 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: 0.290 AC: 44072 AN: 151894 Hom.: 9346 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.291 AC: 44168 AN: 152014 Hom.: 9382 Cov.: 32 AF XY: 0.291 AC XY: 21591 AN XY: 74298

African (AFR) AF: 0.599 AC: 24839 AN: 41438

American (AMR) AF: 0.245 AC: 3739 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3466

East Asian (EAS) AF: 0.264 AC: 1364 AN: 5168

South Asian (SAS) AF: 0.252 AC: 1208 AN: 4802

European-Finnish (FIN) AF: 0.190 AC: 2012 AN: 10572

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9498 AN: 67978

Other (OTH) AF: 0.240 AC: 504 AN: 2100

Alfa AF: 0.187 Hom.: 15124

Bravo AF: 0.304

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.30
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs7547997; hg19: chr1-158341273;