chr6-138155894-A-C

Variant names:

• chr6-138155894-A-C
• rs1883468

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 0.502 in 152,068 control chromosomes in the GnomAD database, including 19,836 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 0.50 (19836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 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: 0.502 AC: 76310 AN: 151950 Hom.: 19793 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.502 AC: 76397 AN: 152068 Hom.: 19836 Cov.: 33 AF XY: 0.500 AC XY: 37165 AN XY: 74332

African (AFR) AF: 0.599 AC: 24867 AN: 41488

American (AMR) AF: 0.493 AC: 7522 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3472

East Asian (EAS) AF: 0.863 AC: 4478 AN: 5186

South Asian (SAS) AF: 0.435 AC: 2097 AN: 4826

European-Finnish (FIN) AF: 0.414 AC: 4371 AN: 10564

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30200 AN: 67948

Other (OTH) AF: 0.485 AC: 1024 AN: 2110

Alfa AF: 0.464 Hom.: 74360

Bravo AF: 0.516

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.38
DANN	Benign	0.58
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1883468; hg19: chr6-138477031;