4-34984506-T-C

Position:

• chr4-34984506-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 0.184 in 151,952 control chromosomes in the GnomAD database, including 2,864 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 0.18 (2864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 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: 0.183 AC: 27847 AN: 151836 Hom.: 2855 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.184 AC: 27891 AN: 151952 Hom.: 2864 Cov.: 32 AF XY: 0.185 AC XY: 13746 AN XY: 74282

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.190

Alfa AF: 0.147 Hom.: 849

Bravo AF: 0.195

Asia WGS AF: 0.231 AC: 805 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16990598; hg19: chr4-34986128;