rs11204897

chr1-151836590-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 0.0882 in 152,200 control chromosomes in the GnomAD database, including 795 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 0.088 (795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.128 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: 0.0883 AC: 13424 AN: 152082 Hom.: 796 Cov.: 31

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0882 AC: 13419 AN: 152200 Hom.: 795 Cov.: 31 AF XY: 0.0874 AC XY: 6503 AN XY: 74426

Gnomad4 AFR AF: 0.0215

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0512

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.106

Alfa AF: 0.120 Hom.: 1235

Bravo AF: 0.0835

Asia WGS AF: 0.0280 AC: 97 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.9
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11204897; hg19: chr1-151809066;