chr6-27263371-A-G

Variant names:

• chr6-27263371-A-G
• rs6938200

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 0.166 in 152,156 control chromosomes in the GnomAD database, including 2,276 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 0.17 (2276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.196 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: 0.166 AC: 25277 AN: 152038 Hom.: 2274 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.166 AC: 25292 AN: 152156 Hom.: 2276 Cov.: 32 AF XY: 0.159 AC XY: 11828 AN XY: 74396

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.148

Alfa AF: 0.178 Hom.: 1172

Bravo AF: 0.167

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.6
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6938200; hg19: chr6-27231150;