6-27281152-T-C

Variant names:

• chr6-27281152-T-C
• rs6932590

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 0.253 in 148,938 control chromosomes in the GnomAD database, including 5,207 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 0.25 (5207 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 89 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.254 AC: 37732 AN: 148838 Hom.: 5200 Cov.: 29

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0284

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.289

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.253 AC: 37745 AN: 148938 Hom.: 5207 Cov.: 29 AF XY: 0.244 AC XY: 17732 AN XY: 72714

African (AFR) AF: 0.345 AC: 13913 AN: 40336

American (AMR) AF: 0.224 AC: 3367 AN: 15014

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 698 AN: 3430

East Asian (EAS) AF: 0.0285 AC: 147 AN: 5156

South Asian (SAS) AF: 0.177 AC: 844 AN: 4772

European-Finnish (FIN) AF: 0.115 AC: 1118 AN: 9750

Middle Eastern (MID) AF: 0.291 AC: 82 AN: 282

European-Non Finnish (NFE) AF: 0.250 AC: 16787 AN: 67214

Other (OTH) AF: 0.260 AC: 541 AN: 2078

Alfa AF: 0.248 Hom.: 22046

Bravo AF: 0.265

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.34
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6932590; hg19: chr6-27248931; COSMIC: COSV70387444;