6-160775768-A-G

Position:

• chr6-160775768-A-G

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 0.411 in 152,048 control chromosomes in the GnomAD database, including 12,945 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 (12945 hom., cov: 32)
• Consequence: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

LOC107986665 (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 (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986665		n.160775768A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000274903	ENST00000619095.1	n.45+1736A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62484 AN: 151930 Hom.: 12937 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.411 AC: 62526 AN: 152048 Hom.: 12945 Cov.: 32 AF XY: 0.410 AC XY: 30443 AN XY: 74300

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.439

Alfa AF: 0.433 Hom.: 27569

Bravo AF: 0.403

Asia WGS AF: 0.416 AC: 1448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1782627; hg19: chr6-161196800;