rs1886249

Positions:

• chr6-121429007-A-G

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 0.192 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.121429007A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.0730

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.177

Alfa AF: 0.151 Hom.: 2564

Bravo AF: 0.196

Asia WGS AF: 0.128 AC: 446 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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