chr4-176651094-A-C

Variant names:

• chr4-176651094-A-C
• rs12498670

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 0.492 in 152,122 control chromosomes in the GnomAD database, including 22,449 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 0.49 (22449 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74840 AN: 152004 Hom.: 22444 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.492 AC: 74855 AN: 152122 Hom.: 22449 Cov.: 33 AF XY: 0.495 AC XY: 36821 AN XY: 74344

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.507

Alfa AF: 0.614 Hom.: 13605

Bravo AF: 0.466

Asia WGS AF: 0.491 AC: 1707 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12498670; hg19: chr4-177572245;