rs1400558

Variant names:

• chr4-147459653-T-C
• rs1400558

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.641 in 152,088 control chromosomes in the GnomAD database, including 32,556 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 0.64 (32556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.722 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: 0.641 AC: 97446 AN: 151968 Hom.: 32545 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.641 AC: 97499 AN: 152088 Hom.: 32556 Cov.: 32 AF XY: 0.645 AC XY: 47961 AN XY: 74342

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.581

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.637

Alfa AF: 0.704 Hom.: 76724

Bravo AF: 0.626

Asia WGS AF: 0.595 AC: 2071 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	0.47
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400558; hg19: chr4-148380805;