rs12190007

Variant names:

• chr6-169327506-G-A
• rs12190007

Your query was ambiguous. Multiple possible variants found:

• chr6-169327506-G-A
• chr6-169327506-G-C
• chr6-169327506-G-T

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 0.376 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.00695

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.367

Alfa AF: 0.406 Hom.: 12473

Bravo AF: 0.362

Asia WGS AF: 0.120 AC: 421 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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