6-28808205-G-C

Variant names:

• chr6-28808205-G-C
• rs1011094

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 0.556 in 152,058 control chromosomes in the GnomAD database, including 24,528 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 0.56 (24528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 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: 0.555 AC: 84387 AN: 151940 Hom.: 24483 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.556 AC: 84484 AN: 152058 Hom.: 24528 Cov.: 32 AF XY: 0.553 AC XY: 41121 AN XY: 74324

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.541

Alfa AF: 0.501 Hom.: 2462

Bravo AF: 0.577

Asia WGS AF: 0.543 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011094; hg19: chr6-28775982;