7-13284548-T-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411542.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229618	ENST00000411542.1	TSL:4	n.237-25661T>G		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.609-25661T>G		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.608-25661T>G		intron	N/A

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

African (AFR) AF: 0.00447 AC: 186 AN: 41574

American (AMR) AF: 0.0244 AC: 373 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0231 AC: 80 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1057 AN: 5174

South Asian (SAS) AF: 0.0935 AC: 451 AN: 4826

European-Finnish (FIN) AF: 0.00668 AC: 71 AN: 10624

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

European-Non Finnish (NFE) AF: 0.0182 AC: 1238 AN: 68000

Other (OTH) AF: 0.0307 AC: 65 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.57
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10488259; hg19: chr7-13324173;