rs11925054

Variant names:

• chr3-55356858-G-T
• rs11925054
• ENST00000809970.1:n.244-4514C>A

Variant summary

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

The ENST00000809970.1(ENSG00000242775):​n.244-4514C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,226 control chromosomes in the GnomAD database, including 856 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 0.097 (856 hom., cov: 32)
• Consequence: ENSG00000242775 ENST00000809970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 3 publications found

Genes affected

ENSG00000242775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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
ENSG00000242775	ENST00000809970.1	n.244-4514C>A		intron_variant	Intron 1 of 3
ENSG00000242775	ENST00000809976.1	n.108-4514C>A		intron_variant	Intron 1 of 1
ENSG00000242775	ENST00000809978.1	n.409-4514C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14777 AN: 152108 Hom.: 857 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0971 AC: 14774 AN: 152226 Hom.: 856 Cov.: 32 AF XY: 0.0932 AC XY: 6935 AN XY: 74424

African (AFR) AF: 0.0488 AC: 2027 AN: 41546

American (AMR) AF: 0.0917 AC: 1402 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3468

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5176

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4826

European-Finnish (FIN) AF: 0.0948 AC: 1004 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8991 AN: 68004

Other (OTH) AF: 0.111 AC: 235 AN: 2114

Alfa AF: 0.123 Hom.: 1572

Bravo AF: 0.0960

Asia WGS AF: 0.0280 AC: 99 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	0.44
DANN	Benign	0.70
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs11925054; hg19: chr3-55390886;