4-51817441-T-C

Position:

• chr4-51817441-T-C

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 0.366 in 151,892 control chromosomes in the GnomAD database, including 11,876 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 0.37 (11876 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55535 AN: 151774 Hom.: 11876 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.366 AC: 55569 AN: 151892 Hom.: 11876 Cov.: 32 AF XY: 0.369 AC XY: 27381 AN XY: 74224

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.301

Alfa AF: 0.264 Hom.: 2653

Bravo AF: 0.368

Asia WGS AF: 0.503 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1910739; hg19: chr4-52683607;