rs463426

Variant names:

• chr22-21454896-T-C
• rs463426

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 0.602 in 151,808 control chromosomes in the GnomAD database, including 28,839 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 0.60 (28839 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.701 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: 0.602 AC: 91369 AN: 151690 Hom.: 28825 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.602 AC: 91428 AN: 151808 Hom.: 28839 Cov.: 32 AF XY: 0.595 AC XY: 44180 AN XY: 74190

African (AFR) AF: 0.461 AC: 19071 AN: 41394

American (AMR) AF: 0.537 AC: 8185 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2259 AN: 3460

East Asian (EAS) AF: 0.487 AC: 2511 AN: 5156

South Asian (SAS) AF: 0.494 AC: 2381 AN: 4816

European-Finnish (FIN) AF: 0.664 AC: 6998 AN: 10546

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47936 AN: 67888

Other (OTH) AF: 0.604 AC: 1270 AN: 2102

Alfa AF: 0.651 Hom.: 85768

Bravo AF: 0.585

Asia WGS AF: 0.443 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.1
DANN	Benign	0.73
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs463426; hg19: chr22-21809185;