1-147524657-A-C

Variant names:

• chr1-147524657-A-C
• rs11240074

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 0.151 in 152,050 control chromosomes in the GnomAD database, including 1,856 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 0.15 (1856 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 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: 0.151 AC: 22869 AN: 151930 Hom.: 1848 Cov.: 31

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0793

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.151 AC: 22909 AN: 152050 Hom.: 1856 Cov.: 31 AF XY: 0.153 AC XY: 11397 AN XY: 74328

African (AFR) AF: 0.186 AC: 7696 AN: 41452

American (AMR) AF: 0.132 AC: 2016 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0793 AC: 275 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1372 AN: 5176

South Asian (SAS) AF: 0.0745 AC: 359 AN: 4820

European-Finnish (FIN) AF: 0.212 AC: 2234 AN: 10562

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8591 AN: 67972

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.135 Hom.: 2710

Bravo AF: 0.148

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.44
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs11240074; hg19: chr1-146996480;