rs1149185

Variant names:

• chr1-111003909-C-T
• rs1149185

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 0.55 in 151,970 control chromosomes in the GnomAD database, including 23,299 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 0.55 (23299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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: 0.550 AC: 83475 AN: 151852 Hom.: 23285 Cov.: 31

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.550 AC: 83521 AN: 151970 Hom.: 23299 Cov.: 31 AF XY: 0.541 AC XY: 40173 AN XY: 74268

African (AFR) AF: 0.599 AC: 24819 AN: 41400

American (AMR) AF: 0.532 AC: 8133 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2135 AN: 3472

East Asian (EAS) AF: 0.363 AC: 1875 AN: 5164

South Asian (SAS) AF: 0.358 AC: 1726 AN: 4818

European-Finnish (FIN) AF: 0.495 AC: 5224 AN: 10560

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37688 AN: 67956

Other (OTH) AF: 0.535 AC: 1128 AN: 2108

Alfa AF: 0.555 Hom.: 79282

Bravo AF: 0.558

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.9
DANN	Benign	0.74
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1149185; hg19: chr1-111546531;