rs467650

Positions:

• chr5-98633749-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 0.397 in 152,018 control chromosomes in the GnomAD database, including 13,935 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 0.40 (13935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 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: 0.397 AC: 60291 AN: 151898 Hom.: 13895 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.397 AC: 60374 AN: 152018 Hom.: 13935 Cov.: 32 AF XY: 0.385 AC XY: 28583 AN XY: 74324

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.0983

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.375

Alfa AF: 0.346 Hom.: 12682

Bravo AF: 0.418

Asia WGS AF: 0.225 AC: 778 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs467650; hg19: chr5-97969453;