chr4-67350255-G-T

Position:

• chr4-67350255-G-T

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 0.0463 in 152,308 control chromosomes in the GnomAD database, including 232 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 0.046 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0664 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: 0.0464 AC: 7062 AN: 152190 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0463 AC: 7057 AN: 152308 Hom.: 232 Cov.: 32 AF XY: 0.0451 AC XY: 3362 AN XY: 74464

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.0639

Gnomad4 FIN AF: 0.0358

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.0491

Alfa AF: 0.0609 Hom.: 83

Bravo AF: 0.0450

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.98
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17088296; hg19: chr4-68215973;