rs7984869

Variant names:

• chr13-86116392-G-T
• rs7984869
• ENST00000445967.1:n.148+43466G>T

Variant summary

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

The ENST00000445967.1(ENSG00000232252):​n.148+43466G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,842 control chromosomes in the GnomAD database, including 27,126 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 0.59 (27126 hom., cov: 31)
• Consequence: ENSG00000232252 ENST00000445967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 4 publications found

Genes affected

ENSG00000232252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 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
ENSG00000232252	ENST00000445967.1	n.148+43466G>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89737 AN: 151724 Hom.: 27092 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.592 AC: 89819 AN: 151842 Hom.: 27126 Cov.: 31 AF XY: 0.591 AC XY: 43850 AN XY: 74210

African (AFR) AF: 0.710 AC: 29397 AN: 41420

American (AMR) AF: 0.536 AC: 8157 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3466

East Asian (EAS) AF: 0.430 AC: 2210 AN: 5136

South Asian (SAS) AF: 0.433 AC: 2082 AN: 4812

European-Finnish (FIN) AF: 0.666 AC: 7033 AN: 10566

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37301 AN: 67900

Other (OTH) AF: 0.553 AC: 1165 AN: 2106

Alfa AF: 0.558 Hom.: 91097

Bravo AF: 0.589

Asia WGS AF: 0.455 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.88
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7984869; hg19: chr13-86690527;