rs11240074

Positions:

• chr1-147524657-A-C
• chr1-147524657-A-G

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 0.151 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0793

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.0745

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.102

Alfa AF: 0.115 Hom.: 510

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11240074; hg19: chr1-146996480;