rs7552806

Variant names:

• chr1-204814890-A-C
• rs7552806

Your query was ambiguous. Multiple possible variants found:

• chr1-204814890-A-C
• chr1-204814890-A-G

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 0.0829 in 152,252 control chromosomes in the GnomAD database, including 1,254 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 0.083 (1254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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: 0.0827 AC: 12589 AN: 152134 Hom.: 1249 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0282

Gnomad FIN AF: 0.00216

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00226

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0829 AC: 12623 AN: 152252 Hom.: 1254 Cov.: 32 AF XY: 0.0838 AC XY: 6244 AN XY: 74480

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0278

Gnomad4 FIN AF: 0.00216

Gnomad4 NFE AF: 0.00226

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0185 Hom.: 253

Bravo AF: 0.0980

Asia WGS AF: 0.101 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7552806; hg19: chr1-204784018;