rs1229119

Variant names:

• chr1-118481017-C-T
• rs1229119

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 0.379 in 151,898 control chromosomes in the GnomAD database, including 11,100 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 (11100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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 (EAS) allele frequency at 95% confidence interval = 0.482 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: 0.379 AC: 57512 AN: 151780 Hom.: 11084 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.379 AC: 57560 AN: 151898 Hom.: 11100 Cov.: 32 AF XY: 0.382 AC XY: 28336 AN XY: 74204

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.385

Alfa AF: 0.388 Hom.: 15392

Bravo AF: 0.376

Asia WGS AF: 0.453 AC: 1575 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.081
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1229119; hg19: chr1-119023640;