chr6-169327506-G-A

Variant names:

• chr6-169327506-G-A
• rs12190007

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 0.376 in 151,974 control chromosomes in the GnomAD database, including 11,545 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 0.38 (11545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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: 0.376 AC: 57136 AN: 151856 Hom.: 11543 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.00713

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.376 AC: 57142 AN: 151974 Hom.: 11545 Cov.: 33 AF XY: 0.371 AC XY: 27572 AN XY: 74268

African (AFR) AF: 0.329 AC: 13623 AN: 41462

American (AMR) AF: 0.294 AC: 4485 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3470

East Asian (EAS) AF: 0.00695 AC: 36 AN: 5178

South Asian (SAS) AF: 0.251 AC: 1206 AN: 4806

European-Finnish (FIN) AF: 0.452 AC: 4758 AN: 10524

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30364 AN: 67960

Other (OTH) AF: 0.367 AC: 772 AN: 2102

Alfa AF: 0.407 Hom.: 15216

Bravo AF: 0.362

Asia WGS AF: 0.120 AC: 421 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.69
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs12190007; hg19: chr6-169727601; COSMIC: COSV69434678;