rs174048

Variant names:

• chr5-143270839-T-C
• rs174048
• ENST00000770709.1:n.117+11546T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000770709.1(ENSG00000300303):​n.117+11546T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,250 control chromosomes in the GnomAD database, including 1,604 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 0.14 (1604 hom., cov: 32)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 14 publications found

Genes affected

ENSG00000300303 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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
ENSG00000300303	ENST00000770709.1	n.117+11546T>C		intron_variant	Intron 1 of 3
ENSG00000300303	ENST00000770710.1	n.117+11546T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20989 AN: 152132 Hom.: 1599 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.0784

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.0331

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.138 AC: 21028 AN: 152250 Hom.: 1604 Cov.: 32 AF XY: 0.137 AC XY: 10192 AN XY: 74438

African (AFR) AF: 0.139 AC: 5762 AN: 41548

American (AMR) AF: 0.0783 AC: 1198 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3466

East Asian (EAS) AF: 0.0707 AC: 367 AN: 5188

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4832

European-Finnish (FIN) AF: 0.211 AC: 2235 AN: 10596

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10630 AN: 68006

Other (OTH) AF: 0.114 AC: 241 AN: 2114

Alfa AF: 0.144 Hom.: 1407

Bravo AF: 0.129

Asia WGS AF: 0.0690 AC: 241 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	6.0
DANN	Benign	0.96
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs174048; hg19: chr5-142650404;