rs11204897

Variant names:

• chr1-151836590-A-G
• rs11204897

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 0.0882 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0215 AC: 895 AN: 41552

American (AMR) AF: 0.0924 AC: 1413 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5176

South Asian (SAS) AF: 0.0512 AC: 247 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1383 AN: 10582

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8869 AN: 68000

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.116 Hom.: 1538

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11204897; hg19: chr1-151809066;