rs6834938

Variant names:

• chr4-182889660-C-T
• rs6834938

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 0.228 in 151,270 control chromosomes in the GnomAD database, including 4,658 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 0.23 (4658 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.228 AC: 34473 AN: 151152 Hom.: 4658 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.228 AC: 34498 AN: 151270 Hom.: 4658 Cov.: 33 AF XY: 0.230 AC XY: 17013 AN XY: 73946

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.221

Alfa AF: 0.168 Hom.: 3041

Bravo AF: 0.239

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6834938; hg19: chr4-183810813;