rs1119231

Positions:

• chr1-186685249-G-A

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 0.196 in 151,904 control chromosomes in the GnomAD database, including 3,836 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 0.20 (3836 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

ACMG classification

Verdict is Benign. Variant got -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 = 0.358 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29745 AN: 151786 Hom.: 3805 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0319

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0471

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.196 AC: 29825 AN: 151904 Hom.: 3836 Cov.: 32 AF XY: 0.191 AC XY: 14167 AN XY: 74264

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0468

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.206

Alfa AF: 0.172 Hom.: 363

Bravo AF: 0.210

Asia WGS AF: 0.168 AC: 586 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1119231; hg19: chr1-186654381;