rs7523477

Positions:

• chr1-205079255-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;