rs4739483

Positions:

• chr8-37219200-T-C
• chr8-37219200-T-G

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 0.442 in 152,102 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 0.44 (16185 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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: 0.442 AC: 67138 AN: 151984 Hom.: 16176 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.442 AC: 67157 AN: 152102 Hom.: 16185 Cov.: 33 AF XY: 0.445 AC XY: 33092 AN XY: 74324

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.434

Alfa AF: 0.498 Hom.: 7472

Bravo AF: 0.426

Asia WGS AF: 0.463 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.79
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4739483; hg19: chr8-37076718;