rs258748

Variant names:

• chr5-143276889-C-G
• rs258748
• ENST00000770709.1:n.118-7810C>G

Variant summary

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

The ENST00000770709.1(ENSG00000300303):​n.118-7810C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,150 control chromosomes in the GnomAD database, including 1,850 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 0.15 (1850 hom., cov: 32)
• Consequence: ENSG00000300303 ENST00000770709.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 6 publications found

Genes affected

ENSG00000300303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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.118-7810C>G		intron_variant	Intron 1 of 3
ENSG00000300303	ENST00000770710.1	n.118-7810C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22543 AN: 152032 Hom.: 1846 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.0719

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.148 AC: 22577 AN: 152150 Hom.: 1850 Cov.: 32 AF XY: 0.146 AC XY: 10894 AN XY: 74362

African (AFR) AF: 0.177 AC: 7338 AN: 41522

American (AMR) AF: 0.0824 AC: 1258 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3468

East Asian (EAS) AF: 0.0719 AC: 373 AN: 5188

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4824

European-Finnish (FIN) AF: 0.203 AC: 2143 AN: 10576

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10616 AN: 67982

Other (OTH) AF: 0.119 AC: 251 AN: 2112

Alfa AF: 0.160 Hom.: 274

Bravo AF: 0.141

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.9
DANN	Benign	0.77
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs258748; hg19: chr5-142656454;