rs10518025

Variant names:

• chr4-67198722-T-C
• rs10518025
• ENST00000754279.1:n.373-8572A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-67198722-T-C
• chr4-67198722-T-G

Variant summary

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

The ENST00000754279.1(ENSG00000298266):​n.373-8572A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,176 control chromosomes in the GnomAD database, including 1,669 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 (1669 hom., cov: 32)
• Consequence: ENSG00000298266 ENST00000754279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792
• Publications: 12 publications found

Genes affected

ENSG00000298266 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 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
ENSG00000298266	ENST00000754279.1	n.373-8572A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21850 AN: 152058 Hom.: 1669 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0787

Gnomad EAS AF: 0.0868

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.144 AC: 21866 AN: 152176 Hom.: 1669 Cov.: 32 AF XY: 0.143 AC XY: 10643 AN XY: 74402

African (AFR) AF: 0.154 AC: 6376 AN: 41530

American (AMR) AF: 0.120 AC: 1832 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0787 AC: 273 AN: 3470

East Asian (EAS) AF: 0.0858 AC: 444 AN: 5174

South Asian (SAS) AF: 0.175 AC: 845 AN: 4826

European-Finnish (FIN) AF: 0.137 AC: 1457 AN: 10600

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10213 AN: 67990

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.141 Hom.: 6846

Bravo AF: 0.141

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.1
DANN	Benign	0.72
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10518025; hg19: chr4-68064440;