1-147886156-A-G

Variant names:

• chr1-147886156-A-G
• rs11240147

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 0.166 in 152,100 control chromosomes in the GnomAD database, including 3,195 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 0.17 (3195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.410
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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: 0.166 AC: 25170 AN: 151984 Hom.: 3187 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0576

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.166 AC: 25216 AN: 152100 Hom.: 3195 Cov.: 32 AF XY: 0.166 AC XY: 12331 AN XY: 74358

African (AFR) AF: 0.338 AC: 14014 AN: 41454

American (AMR) AF: 0.174 AC: 2660 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3462

East Asian (EAS) AF: 0.318 AC: 1646 AN: 5180

South Asian (SAS) AF: 0.200 AC: 964 AN: 4816

European-Finnish (FIN) AF: 0.0576 AC: 610 AN: 10592

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0714 AC: 4856 AN: 68008

Other (OTH) AF: 0.141 AC: 298 AN: 2108

Alfa AF: 0.0984 Hom.: 1711

Bravo AF: 0.182

Asia WGS AF: 0.284 AC: 985 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.38
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11240147; hg19: chr1-147358281;