4-42819494-T-C

Variant names:

• chr4-42819494-T-C
• rs1584622

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 0.596 in 152,060 control chromosomes in the GnomAD database, including 27,823 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 (27823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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: 0.596 AC: 90560 AN: 151942 Hom.: 27810 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.596 AC: 90624 AN: 152060 Hom.: 27823 Cov.: 32 AF XY: 0.600 AC XY: 44583 AN XY: 74324

African (AFR) AF: 0.464 AC: 19234 AN: 41474

American (AMR) AF: 0.646 AC: 9869 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3470

East Asian (EAS) AF: 0.899 AC: 4647 AN: 5170

South Asian (SAS) AF: 0.652 AC: 3142 AN: 4818

European-Finnish (FIN) AF: 0.645 AC: 6821 AN: 10580

Middle Eastern (MID) AF: 0.497 AC: 144 AN: 290

European-Non Finnish (NFE) AF: 0.633 AC: 42987 AN: 67960

Other (OTH) AF: 0.608 AC: 1282 AN: 2110

Alfa AF: 0.617 Hom.: 91448

Bravo AF: 0.589

Asia WGS AF: 0.738 AC: 2564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1584622; hg19: chr4-42821511;