rs7989848

Variant names:

• chr13-109631121-G-A
• rs7989848
• ENST00000650264.1:n.759-59963C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-109631121-G-A
• chr13-109631121-G-C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-59963C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,046 control chromosomes in the GnomAD database, including 17,631 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 0.47 (17631 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 7 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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
ENSG00000285534	ENST00000650264.1	n.759-59963C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72000 AN: 151928 Hom.: 17624 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.474 AC: 72040 AN: 152046 Hom.: 17631 Cov.: 32 AF XY: 0.470 AC XY: 34895 AN XY: 74312

African (AFR) AF: 0.365 AC: 15147 AN: 41452

American (AMR) AF: 0.414 AC: 6324 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1901 AN: 3464

East Asian (EAS) AF: 0.372 AC: 1919 AN: 5156

South Asian (SAS) AF: 0.368 AC: 1775 AN: 4826

European-Finnish (FIN) AF: 0.592 AC: 6265 AN: 10578

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36869 AN: 67964

Other (OTH) AF: 0.484 AC: 1023 AN: 2114

Alfa AF: 0.512 Hom.: 64444

Bravo AF: 0.460

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.41
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs7989848; hg19: chr13-110283468;