4-122148684-G-A

Position:

• chr4-122148684-G-A

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 0.249 in 152,030 control chromosomes in the GnomAD database, including 5,695 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 0.25 (5695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37805 AN: 151912 Hom.: 5684 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.249 AC: 37838 AN: 152030 Hom.: 5695 Cov.: 32 AF XY: 0.255 AC XY: 18917 AN XY: 74290

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.299

Alfa AF: 0.302 Hom.: 3575

Bravo AF: 0.238

Asia WGS AF: 0.406 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6835946; hg19: chr4-123069839;