4-68749350-A-G

Position:

• chr4-68749350-A-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 0.354 in 152,122 control chromosomes in the GnomAD database, including 11,587 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 0.35 (11587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53736 AN: 152004 Hom.: 11556 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.354 AC: 53839 AN: 152122 Hom.: 11587 Cov.: 33 AF XY: 0.358 AC XY: 26615 AN XY: 74370

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.218

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.356

Alfa AF: 0.297 Hom.: 1083

Bravo AF: 0.381

Asia WGS AF: 0.259 AC: 902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs429247; hg19: chr4-69615068;