rs1954548

Variant names:

• chr14-57177800-G-A
• rs1954548
• ENST00000825124.1:n.227+9023C>T

Variant summary

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

The ENST00000825124.1(ENSG00000307333):​n.227+9023C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 152,200 control chromosomes in the GnomAD database, including 1,516 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 0.095 (1516 hom., cov: 33)
• Consequence: ENSG00000307333 ENST00000825124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 1 publications found

Genes affected

ENSG00000307333 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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
ENSG00000307333	ENST00000825124.1	n.227+9023C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0948 AC: 14413 AN: 152082 Hom.: 1513 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0949 AC: 14440 AN: 152200 Hom.: 1516 Cov.: 33 AF XY: 0.0931 AC XY: 6928 AN XY: 74428

African (AFR) AF: 0.260 AC: 10771 AN: 41494

American (AMR) AF: 0.0435 AC: 666 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 72 AN: 3468

East Asian (EAS) AF: 0.0922 AC: 478 AN: 5182

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4824

European-Finnish (FIN) AF: 0.0144 AC: 153 AN: 10602

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0266 AC: 1807 AN: 68016

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0499 Hom.: 196

Bravo AF: 0.105

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.35
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs1954548; hg19: chr14-57644518;