chr6-138123793-A-G

Variant names:

• chr6-138123793-A-G
• rs6922466

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 0.211 in 152,070 control chromosomes in the GnomAD database, including 3,657 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 0.21 (3657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 17 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 (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.211 AC: 32005 AN: 151952 Hom.: 3651 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.211 AC: 32035 AN: 152070 Hom.: 3657 Cov.: 32 AF XY: 0.208 AC XY: 15454 AN XY: 74336

African (AFR) AF: 0.171 AC: 7112 AN: 41480

American (AMR) AF: 0.184 AC: 2808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3466

East Asian (EAS) AF: 0.181 AC: 937 AN: 5172

South Asian (SAS) AF: 0.418 AC: 2012 AN: 4812

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10582

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16082 AN: 67968

Other (OTH) AF: 0.236 AC: 498 AN: 2114

Alfa AF: 0.235 Hom.: 7236

Bravo AF: 0.206

Asia WGS AF: 0.318 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.47
DANN	Benign	0.57
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs6922466; hg19: chr6-138444930;