rs1400558

Variant names:

• chr4-147459653-T-C
• rs1400558

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 0.641 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

African (AFR) AF: 0.441 AC: 18280 AN: 41482

American (AMR) AF: 0.730 AC: 11160 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2033 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3345 AN: 5138

South Asian (SAS) AF: 0.581 AC: 2801 AN: 4824

European-Finnish (FIN) AF: 0.781 AC: 8278 AN: 10598

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49470 AN: 67984

Other (OTH) AF: 0.637 AC: 1341 AN: 2106

Alfa AF: 0.692 Hom.: 153620

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1400558; hg19: chr4-148380805;