rs6848139

chr4-122473886-A-Cchr4-122473886-A-G

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 0.164 in 151,994 control chromosomes in the GnomAD database, including 3,590 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 0.16 (3590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.163 AC: 24814 AN: 151876 Hom.: 3577 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0544

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.0954

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0824

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.164 AC: 24852 AN: 151994 Hom.: 3590 Cov.: 32 AF XY: 0.162 AC XY: 12003 AN XY: 74320

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.0544

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0617

Gnomad4 FIN AF: 0.0954

Gnomad4 NFE AF: 0.0823

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0847 Hom.: 1104

Bravo AF: 0.170

Asia WGS AF: 0.0540 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.45
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: rs6848139; hg19: chr4-123395041;