4-36492983-T-A

Position:

• chr4-36492983-T-A

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 0.105 in 152,134 control chromosomes in the GnomAD database, including 1,668 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 0.10 (1668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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: 0.105 AC: 15939 AN: 152016 Hom.: 1673 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0237

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.105 AC: 15952 AN: 152134 Hom.: 1668 Cov.: 32 AF XY: 0.104 AC XY: 7700 AN XY: 74394

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0237

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.0306

Gnomad4 OTH AF: 0.0847

Alfa AF: 0.0712 Hom.: 118

Bravo AF: 0.124

Asia WGS AF: 0.0820 AC: 285 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6850219; hg19: chr4-36494605;