chr4-10179199-C-T

Variant names:

• chr4-10179199-C-T
• rs6811287

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 0.425 in 151,966 control chromosomes in the GnomAD database, including 13,938 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 0.42 (13938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.424 AC: 64453 AN: 151848 Hom.: 13919 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.425 AC: 64510 AN: 151966 Hom.: 13938 Cov.: 32 AF XY: 0.429 AC XY: 31844 AN XY: 74278

African (AFR) AF: 0.341 AC: 14120 AN: 41446

American (AMR) AF: 0.471 AC: 7204 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2253 AN: 5146

South Asian (SAS) AF: 0.629 AC: 3017 AN: 4800

European-Finnish (FIN) AF: 0.458 AC: 4831 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30283 AN: 67964

Other (OTH) AF: 0.427 AC: 900 AN: 2110

Alfa AF: 0.442 Hom.: 57245

Bravo AF: 0.417

Asia WGS AF: 0.538 AC: 1865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.39
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6811287; hg19: chr4-10180823;