rs7326634

Variant names:

• chr13-86166464-C-A
• rs7326634
• ENST00000445967.1:n.149-4381C>A

Your query was ambiguous. Multiple possible variants found:

• chr13-86166464-C-A
• chr13-86166464-C-T

Variant summary

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

The ENST00000445967.1(ENSG00000232252):​n.149-4381C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,992 control chromosomes in the GnomAD database, including 21,480 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 0.53 (21480 hom., cov: 32)
• Consequence: ENSG00000232252 ENST00000445967.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 6 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 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.149-4381C>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80485 AN: 151874 Hom.: 21455 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.530 AC: 80572 AN: 151992 Hom.: 21480 Cov.: 32 AF XY: 0.530 AC XY: 39341 AN XY: 74276

African (AFR) AF: 0.540 AC: 22365 AN: 41448

American (AMR) AF: 0.483 AC: 7361 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1633 AN: 3464

East Asian (EAS) AF: 0.553 AC: 2851 AN: 5160

South Asian (SAS) AF: 0.480 AC: 2313 AN: 4820

European-Finnish (FIN) AF: 0.588 AC: 6215 AN: 10566

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36079 AN: 67970

Other (OTH) AF: 0.514 AC: 1084 AN: 2110

Alfa AF: 0.522 Hom.: 82769

Bravo AF: 0.523

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.67
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs7326634; hg19: chr13-86740599;