4-4889421-C-T

Variant names:

• chr4-4889421-C-T
• rs6817411

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 0.563 in 152,110 control chromosomes in the GnomAD database, including 24,903 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 0.56 (24903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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: 0.563 AC: 85518 AN: 151992 Hom.: 24858 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.563 AC: 85617 AN: 152110 Hom.: 24903 Cov.: 33 AF XY: 0.572 AC XY: 42555 AN XY: 74356

African (AFR) AF: 0.680 AC: 28213 AN: 41506

American (AMR) AF: 0.556 AC: 8492 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3468

East Asian (EAS) AF: 0.784 AC: 4051 AN: 5166

South Asian (SAS) AF: 0.566 AC: 2728 AN: 4818

European-Finnish (FIN) AF: 0.635 AC: 6729 AN: 10600

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32118 AN: 67950

Other (OTH) AF: 0.541 AC: 1143 AN: 2112

Alfa AF: 0.499 Hom.: 74348

Bravo AF: 0.559

Asia WGS AF: 0.673 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.95
DANN	Benign	0.41
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6817411; hg19: chr4-4891148;