rs7521536

Positions:

• chr1-173496126-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 0.22 in 152,058 control chromosomes in the GnomAD database, including 3,969 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 0.22 (3969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 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: 0.220 AC: 33382 AN: 151940 Hom.: 3951 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.220 AC: 33453 AN: 152058 Hom.: 3969 Cov.: 32 AF XY: 0.218 AC XY: 16179 AN XY: 74364

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.215

Alfa AF: 0.196 Hom.: 3744

Bravo AF: 0.230

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7521536; hg19: chr1-173465265;