6-90512091-T-C

Variant names:

• chr6-90512091-T-C
• rs806287

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 0.217 in 152,052 control chromosomes in the GnomAD database, including 4,175 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 0.22 (4175 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 4 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 (NFE) allele frequency at 95% confidence interval = 0.284 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: 0.217 AC: 33027 AN: 151934 Hom.: 4177 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.217 AC: 33019 AN: 152052 Hom.: 4175 Cov.: 31 AF XY: 0.217 AC XY: 16103 AN XY: 74320

African (AFR) AF: 0.107 AC: 4450 AN: 41504

American (AMR) AF: 0.176 AC: 2678 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3470

East Asian (EAS) AF: 0.101 AC: 524 AN: 5176

South Asian (SAS) AF: 0.158 AC: 759 AN: 4818

European-Finnish (FIN) AF: 0.323 AC: 3416 AN: 10560

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19531 AN: 67960

Other (OTH) AF: 0.227 AC: 480 AN: 2112

Alfa AF: 0.261 Hom.: 6926

Bravo AF: 0.202

Asia WGS AF: 0.160 AC: 556 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	1.1
DANN	Benign	0.42
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs806287; hg19: chr6-91221810; COSMIC: COSV65225762;