chr6-121429007-A-G

Variant names:

• chr6-121429007-A-G
• rs1886249

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 0.192 in 152,168 control chromosomes in the GnomAD database, including 3,449 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 0.19 (3449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 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: 0.192 AC: 29215 AN: 152050 Hom.: 3448 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0730

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.192 AC: 29234 AN: 152168 Hom.: 3449 Cov.: 32 AF XY: 0.189 AC XY: 14065 AN XY: 74406

African (AFR) AF: 0.348 AC: 14447 AN: 41468

American (AMR) AF: 0.109 AC: 1666 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3472

East Asian (EAS) AF: 0.0730 AC: 379 AN: 5194

South Asian (SAS) AF: 0.174 AC: 838 AN: 4818

European-Finnish (FIN) AF: 0.117 AC: 1244 AN: 10610

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9525 AN: 68004

Other (OTH) AF: 0.177 AC: 374 AN: 2114

Alfa AF: 0.155 Hom.: 6040

Bravo AF: 0.196

Asia WGS AF: 0.128 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.50
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1886249; hg19: chr6-121750153; COSMIC: COSV69423780;