rs7556447

Variant names:

• chr1-2414660-C-G
• rs7556447

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 0.199 in 152,212 control chromosomes in the GnomAD database, including 3,505 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 0.20 (3505 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.200 AC: 30353 AN: 152094 Hom.: 3505 Cov.: 33

Gnomad AFR AF: 0.0985

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.199 AC: 30352 AN: 152212 Hom.: 3505 Cov.: 33 AF XY: 0.201 AC XY: 14974 AN XY: 74420

Gnomad4 AFR AF: 0.0983

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.211

Alfa AF: 0.230 Hom.: 535

Bravo AF: 0.183

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7556447; hg19: chr1-2346099;