7-13284548-T-G

Variant names:

• chr7-13284548-T-G
• rs10488259
• ENST00000411542.1:n.237-25661T>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000411542.1(ENSG00000229618):​n.237-25661T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,294 control chromosomes in the GnomAD database, including 157 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 0.024 (157 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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
ENSG00000229618	ENST00000411542.1	n.237-25661T>G		intron_variant	Intron 2 of 4	4
ENSG00000229618	ENST00000638964.1	n.609-25661T>G		intron_variant	Intron 2 of 5	5
ENSG00000229618	ENST00000639998.1	n.608-25661T>G		intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0239 AC: 3631 AN: 152176 Hom.: 161 Cov.: 32

Gnomad AFR AF: 0.00449

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0244

Gnomad ASJ AF: 0.0231

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.00668

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0237 AC: 3616 AN: 152294 Hom.: 157 Cov.: 32 AF XY: 0.0255 AC XY: 1896 AN XY: 74460

Gnomad4 AFR AF: 0.00447

Gnomad4 AMR AF: 0.0244

Gnomad4 ASJ AF: 0.0231

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.0935

Gnomad4 FIN AF: 0.00668

Gnomad4 NFE AF: 0.0182

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0172 Hom.: 3

Bravo AF: 0.0241

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488259; hg19: chr7-13324173;