6-115043709-G-T

Variant names:

• chr6-115043709-G-T
• rs189411

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 0.398 in 151,658 control chromosomes in the GnomAD database, including 14,371 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 0.40 (14371 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60303 AN: 151544 Hom.: 14354 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.398 AC: 60355 AN: 151658 Hom.: 14371 Cov.: 31 AF XY: 0.396 AC XY: 29313 AN XY: 74080

African (AFR) AF: 0.663 AC: 27447 AN: 41372

American (AMR) AF: 0.264 AC: 4022 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 942 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1574 AN: 5154

South Asian (SAS) AF: 0.479 AC: 2306 AN: 4812

European-Finnish (FIN) AF: 0.273 AC: 2845 AN: 10434

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20063 AN: 67860

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.361 Hom.: 1983

Bravo AF: 0.406

Asia WGS AF: 0.385 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.61
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs189411; hg19: chr6-115364873;