rs1424854

Variant names:

• chr9-21217850-C-T
• rs1424854

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 0.195 in 151,930 control chromosomes in the GnomAD database, including 3,137 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 0.19 (3137 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 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: 0.195 AC: 29532 AN: 151810 Hom.: 3134 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.144

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.195 AC: 29560 AN: 151930 Hom.: 3137 Cov.: 32 AF XY: 0.195 AC XY: 14501 AN XY: 74236

African (AFR) AF: 0.202 AC: 8367 AN: 41444

American (AMR) AF: 0.245 AC: 3733 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2136 AN: 5162

South Asian (SAS) AF: 0.113 AC: 546 AN: 4820

European-Finnish (FIN) AF: 0.192 AC: 2017 AN: 10530

Middle Eastern (MID) AF: 0.141 AC: 41 AN: 290

European-Non Finnish (NFE) AF: 0.169 AC: 11483 AN: 67948

Other (OTH) AF: 0.193 AC: 407 AN: 2108

Alfa AF: 0.188 Hom.: 341

Bravo AF: 0.201

Asia WGS AF: 0.248 AC: 854 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.42
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1424854; hg19: chr9-21217849;