chr6-27168446-A-G

Variant names:

• chr6-27168446-A-G
• rs13219181

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 0.14 in 152,212 control chromosomes in the GnomAD database, including 1,631 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 0.14 (1631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 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: 0.140 AC: 21270 AN: 152092 Hom.: 1631 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.00852

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.140 AC: 21270 AN: 152212 Hom.: 1631 Cov.: 32 AF XY: 0.133 AC XY: 9914 AN XY: 74442

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.00854

Gnomad4 SAS AF: 0.0921

Gnomad4 FIN AF: 0.0901

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.124

Alfa AF: 0.163 Hom.: 551

Bravo AF: 0.142

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13219181; hg19: chr6-27136225;