rs11577354

Variant names:

• chr1-235103812-G-A
• rs11577354

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 0.53 in 150,816 control chromosomes in the GnomAD database, including 21,437 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 0.53 (21437 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

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 (SAS) allele frequency at 95% confidence interval = 0.575 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: 0.530 AC: 79929 AN: 150734 Hom.: 21424 Cov.: 28

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.530 AC: 79984 AN: 150816 Hom.: 21437 Cov.: 28 AF XY: 0.534 AC XY: 39258 AN XY: 73554

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.485

Alfa AF: 0.511 Hom.: 19320

Bravo AF: 0.520

Asia WGS AF: 0.486 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
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: rs11577354; hg19: chr1-235267127;