rs346101

Variant names:

• chr4-178683058-G-A
• rs346101

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 0.359 in 152,100 control chromosomes in the GnomAD database, including 11,030 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 0.36 (11030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 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: 0.360 AC: 54656 AN: 151982 Hom.: 11029 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.00983

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.359 AC: 54672 AN: 152100 Hom.: 11030 Cov.: 32 AF XY: 0.354 AC XY: 26353 AN XY: 74370

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.0101

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.355

Alfa AF: 0.425 Hom.: 13731

Bravo AF: 0.340

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346101; hg19: chr4-179604212; COSMIC: COSV66887991;