chr6-20382369-G-A

Variant names:

• chr6-20382369-G-A
• rs1570155

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 0.634 in 151,138 control chromosomes in the GnomAD database, including 31,714 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 0.63 (31714 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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: 0.634 AC: 95673 AN: 151020 Hom.: 31665 Cov.: 31

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.634 AC: 95786 AN: 151138 Hom.: 31714 Cov.: 31 AF XY: 0.622 AC XY: 45932 AN XY: 73822

African (AFR) AF: 0.845 AC: 34889 AN: 41300

American (AMR) AF: 0.483 AC: 7334 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1894 AN: 3442

East Asian (EAS) AF: 0.446 AC: 2252 AN: 5054

South Asian (SAS) AF: 0.470 AC: 2247 AN: 4776

European-Finnish (FIN) AF: 0.535 AC: 5619 AN: 10504

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39422 AN: 67604

Other (OTH) AF: 0.613 AC: 1277 AN: 2084

Alfa AF: 0.595 Hom.: 93911

Bravo AF: 0.641

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.36
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1570155; hg19: chr6-20382600;