rs467650

Variant names:

• chr5-98633749-T-C
• rs467650

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.634 AC: 26261 AN: 41424

American (AMR) AF: 0.306 AC: 4682 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3470

East Asian (EAS) AF: 0.0983 AC: 509 AN: 5180

South Asian (SAS) AF: 0.245 AC: 1184 AN: 4828

European-Finnish (FIN) AF: 0.212 AC: 2235 AN: 10556

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22855 AN: 67956

Other (OTH) AF: 0.375 AC: 792 AN: 2114

Alfa AF: 0.354 Hom.: 30473

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
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs467650; hg19: chr5-97969453;