4-108038126-A-G

Variant names:

• chr4-108038126-A-G
• rs6851442

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 0.116 in 152,232 control chromosomes in the GnomAD database, including 1,578 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 0.12 (1578 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17702 AN: 152114 Hom.: 1578 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.116 AC: 17715 AN: 152232 Hom.: 1578 Cov.: 32 AF XY: 0.113 AC XY: 8424 AN XY: 74446

African (AFR) AF: 0.244 AC: 10112 AN: 41512

American (AMR) AF: 0.0635 AC: 971 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3472

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5180

South Asian (SAS) AF: 0.0973 AC: 469 AN: 4820

European-Finnish (FIN) AF: 0.0374 AC: 397 AN: 10610

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0775 AC: 5270 AN: 68028

Other (OTH) AF: 0.0946 AC: 200 AN: 2114

Alfa AF: 0.0776 Hom.: 1077

Bravo AF: 0.121

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.74
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6851442; hg19: chr4-108959282;