6-164624301-G-T

Variant names:

• chr6-164624301-G-T
• rs727811

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 0.468 in 151,830 control chromosomes in the GnomAD database, including 17,916 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 0.47 (17916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

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 (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.469 AC: 71089 AN: 151710 Hom.: 17916 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.468 AC: 71113 AN: 151830 Hom.: 17916 Cov.: 32 AF XY: 0.467 AC XY: 34672 AN XY: 74182

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.498

Alfa AF: 0.539 Hom.: 29620

Bravo AF: 0.459

Asia WGS AF: 0.581 AC: 2013 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727811; hg19: chr6-165045334;