6-155727330-G-A

Position:

• chr6-155727330-G-A

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 0.413 in 151,448 control chromosomes in the GnomAD database, including 13,234 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 0.41 (13234 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.155727330G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62521 AN: 151330 Hom.: 13222 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.413 AC: 62545 AN: 151448 Hom.: 13234 Cov.: 32 AF XY: 0.420 AC XY: 31091 AN XY: 73994

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.403

Alfa AF: 0.353 Hom.: 1369

Bravo AF: 0.403

Asia WGS AF: 0.392 AC: 1347 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1498637; hg19: chr6-156048464;