rs3847554

Variant names:

• chr11-92935660-C-T
• rs3847554
• ENST00000532770.2:n.146+4654C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532770.2(ENSG00000254874):​n.146+4654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,056 control chromosomes in the GnomAD database, including 25,967 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 0.55 (25967 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 22 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 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
ENSG00000254874	ENST00000532770.2	n.146+4654C>T		intron_variant	Intron 1 of 3	2
ENSG00000254874	ENST00000749785.1	n.128+4654C>T		intron_variant	Intron 1 of 2
ENSG00000254874	ENST00000749786.1	n.115+4654C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83756 AN: 151938 Hom.: 25925 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.551 AC: 83851 AN: 152056 Hom.: 25967 Cov.: 32 AF XY: 0.550 AC XY: 40901 AN XY: 74322

African (AFR) AF: 0.859 AC: 35633 AN: 41502

American (AMR) AF: 0.392 AC: 5983 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1529 AN: 3462

East Asian (EAS) AF: 0.530 AC: 2734 AN: 5162

South Asian (SAS) AF: 0.514 AC: 2484 AN: 4828

European-Finnish (FIN) AF: 0.491 AC: 5179 AN: 10550

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28500 AN: 67966

Other (OTH) AF: 0.531 AC: 1123 AN: 2114

Alfa AF: 0.460 Hom.: 53100

Bravo AF: 0.557

Asia WGS AF: 0.487 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs3847554; hg19: chr11-92668826;