chr6-28900023-C-T

Variant names:

• chr6-28900023-C-T
• rs209130

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 0.61 in 152,024 control chromosomes in the GnomAD database, including 30,576 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 0.61 (30576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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: 0.610 AC: 92602 AN: 151906 Hom.: 30516 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.610 AC: 92710 AN: 152024 Hom.: 30576 Cov.: 32 AF XY: 0.605 AC XY: 44966 AN XY: 74272

African (AFR) AF: 0.871 AC: 36171 AN: 41530

American (AMR) AF: 0.579 AC: 8839 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3470

East Asian (EAS) AF: 0.657 AC: 3394 AN: 5166

South Asian (SAS) AF: 0.579 AC: 2786 AN: 4808

European-Finnish (FIN) AF: 0.404 AC: 4260 AN: 10536

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33380 AN: 67948

Other (OTH) AF: 0.607 AC: 1283 AN: 2112

Alfa AF: 0.543 Hom.: 22976

Bravo AF: 0.640

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.39
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs209130; hg19: chr6-28867800;