rs7523477

Variant names:

• chr1-205079255-T-C
• rs7523477

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 0.799 in 152,126 control chromosomes in the GnomAD database, including 49,816 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 0.80 (49816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

ACMG classification

Verdict is Benign. Variant got -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 = 0.947 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: 0.800 AC: 121560 AN: 152008 Hom.: 49800 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.799 AC: 121616 AN: 152126 Hom.: 49816 Cov.: 32 AF XY: 0.803 AC XY: 59736 AN XY: 74370

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.970

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.843

Alfa AF: 0.856 Hom.: 73519

Bravo AF: 0.793

Asia WGS AF: 0.928 AC: 3228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7523477; hg19: chr1-205048383;