4-66491736-A-C

Position:

• chr4-66491736-A-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 0.0622 in 152,222 control chromosomes in the GnomAD database, including 298 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 0.062 (298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0724 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: 0.0622 AC: 9467 AN: 152104 Hom.: 299 Cov.: 32

Gnomad AFR AF: 0.0746

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0182

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.0827

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0622 AC: 9470 AN: 152222 Hom.: 298 Cov.: 32 AF XY: 0.0612 AC XY: 4554 AN XY: 74438

Gnomad4 AFR AF: 0.0746

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.0182

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.0341

Gnomad4 FIN AF: 0.0827

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0491

Alfa AF: 0.0336 Hom.: 25

Bravo AF: 0.0598

Asia WGS AF: 0.0210 AC: 74 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.7
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17730929; hg19: chr4-67357454;