rs6838036

Variant names:

• chr4-108489923-C-A
• rs6838036

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 0.721 in 152,026 control chromosomes in the GnomAD database, including 39,856 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 0.72 (39856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.721 AC: 109514 AN: 151908 Hom.: 39809 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.721 AC: 109621 AN: 152026 Hom.: 39856 Cov.: 32 AF XY: 0.726 AC XY: 53950 AN XY: 74298

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.715

Alfa AF: 0.699 Hom.: 63919

Bravo AF: 0.729

Asia WGS AF: 0.923 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6838036; hg19: chr4-109411079;