4-46131526-C-T

Variant names:

• chr4-46131526-C-T
• rs17639557

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 0.416 in 151,818 control chromosomes in the GnomAD database, including 13,767 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 0.42 (13767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.416 AC: 63111 AN: 151700 Hom.: 13762 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.416 AC: 63141 AN: 151818 Hom.: 13767 Cov.: 32 AF XY: 0.412 AC XY: 30552 AN XY: 74160

African (AFR) AF: 0.319 AC: 13213 AN: 41406

American (AMR) AF: 0.405 AC: 6159 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1581 AN: 5152

South Asian (SAS) AF: 0.298 AC: 1433 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4886 AN: 10546

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33231 AN: 67918

Other (OTH) AF: 0.412 AC: 868 AN: 2108

Alfa AF: 0.448 Hom.: 3725

Bravo AF: 0.408

Asia WGS AF: 0.292 AC: 1015 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs17639557; hg19: chr4-46133543;