rs6835946

Variant names:

• chr4-122148684-G-A
• rs6835946

Your query was ambiguous. Multiple possible variants found:

• chr4-122148684-G-A
• chr4-122148684-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0737 AC: 3058 AN: 41508

American (AMR) AF: 0.295 AC: 4505 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1456 AN: 3472

East Asian (EAS) AF: 0.367 AC: 1890 AN: 5156

South Asian (SAS) AF: 0.482 AC: 2321 AN: 4814

European-Finnish (FIN) AF: 0.295 AC: 3110 AN: 10538

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20411 AN: 67950

Other (OTH) AF: 0.299 AC: 630 AN: 2110

Alfa AF: 0.300 Hom.: 3958

Bravo AF: 0.238

Asia WGS AF: 0.406 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.7
DANN	Benign	0.70
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs6835946; hg19: chr4-123069839;