rs7547997

Variant names:

• chr1-158371483-G-A
• rs7547997

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.599

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.240

Alfa AF: 0.165 Hom.: 4596

Bravo AF: 0.304

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7547997; hg19: chr1-158341273;