rs6848139

Variant names:

• chr4-122473886-A-C
• rs6848139

Your query was ambiguous. Multiple possible variants found:

• chr4-122473886-A-C
• chr4-122473886-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;