rs11240147

Positions:

• chr1-147886156-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 0.166 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

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 (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0576

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0881 Hom.: 976

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11240147; hg19: chr1-147358281;