rs460

Positions:

• chr7-97784798-C-T

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 0.261 in 151,946 control chromosomes in the GnomAD database, including 5,856 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 0.26 (5856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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: 0.261 AC: 39558 AN: 151828 Hom.: 5852 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.261 AC: 39608 AN: 151946 Hom.: 5856 Cov.: 32 AF XY: 0.255 AC XY: 18959 AN XY: 74286

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.264

Alfa AF: 0.222 Hom.: 7827

Bravo AF: 0.270

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs460; hg19: chr7-97414110;