rs1119231

Variant names:

• chr1-186685249-G-A
• rs1119231

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;