6-160808546-T-G

Variant names:

• chr6-160808546-T-G
• rs783153

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.568 in 151,740 control chromosomes in the GnomAD database, including 25,188 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 0.57 (25188 hom., cov: 30)
• Consequence: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 5 publications found

Genes affected

LOC107986665 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86157 AN: 151622 Hom.: 25156 Cov.: 30

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.568 AC: 86244 AN: 151740 Hom.: 25188 Cov.: 30 AF XY: 0.574 AC XY: 42590 AN XY: 74152

African (AFR) AF: 0.560 AC: 23172 AN: 41384

American (AMR) AF: 0.664 AC: 10111 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1690 AN: 3456

East Asian (EAS) AF: 0.975 AC: 5010 AN: 5136

South Asian (SAS) AF: 0.681 AC: 3272 AN: 4804

European-Finnish (FIN) AF: 0.518 AC: 5450 AN: 10530

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35650 AN: 67904

Other (OTH) AF: 0.587 AC: 1236 AN: 2106

Alfa AF: 0.571 Hom.: 4377

Bravo AF: 0.580

Asia WGS AF: 0.818 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.47
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs783153; hg19: chr6-161229578;