4-57902288-C-T

Variant names:

• chr4-57902288-C-T
• rs10517418

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 0.454 in 151,840 control chromosomes in the GnomAD database, including 16,185 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 0.45 (16185 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 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: 0.454 AC: 68857 AN: 151722 Hom.: 16158 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.454 AC: 68939 AN: 151840 Hom.: 16185 Cov.: 32 AF XY: 0.451 AC XY: 33496 AN XY: 74206

African (AFR) AF: 0.548 AC: 22701 AN: 41394

American (AMR) AF: 0.526 AC: 8031 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1360 AN: 3464

East Asian (EAS) AF: 0.498 AC: 2559 AN: 5140

South Asian (SAS) AF: 0.310 AC: 1490 AN: 4812

European-Finnish (FIN) AF: 0.354 AC: 3730 AN: 10540

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27533 AN: 67926

Other (OTH) AF: 0.477 AC: 1003 AN: 2104

Alfa AF: 0.424 Hom.: 58325

Bravo AF: 0.474

Asia WGS AF: 0.422 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.55
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs10517418; hg19: chr4-58768454;