rs7332384

Variant names:

• chr13-26799017-G-A
• rs7332384
• ENST00000766962.1:n.267+985G>A

Variant summary

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

The ENST00000766962.1(ENSG00000299861):​n.267+985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,056 control chromosomes in the GnomAD database, including 12,905 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 0.41 (12905 hom., cov: 32)
• Consequence: ENSG00000299861 ENST00000766962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 2 publications found

Genes affected

ENSG00000299861 (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 (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766962.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299861	ENST00000766962.1		n.267+985G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61686 AN: 151938 Hom.: 12894 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.406 AC: 61728 AN: 152056 Hom.: 12905 Cov.: 32 AF XY: 0.408 AC XY: 30323 AN XY: 74328

African (AFR) AF: 0.308 AC: 12787 AN: 41464

American (AMR) AF: 0.412 AC: 6298 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3468

East Asian (EAS) AF: 0.625 AC: 3232 AN: 5172

South Asian (SAS) AF: 0.476 AC: 2293 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4312 AN: 10564

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29867 AN: 67978

Other (OTH) AF: 0.412 AC: 870 AN: 2114

Alfa AF: 0.430 Hom.: 61179

Bravo AF: 0.401

Asia WGS AF: 0.523 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.84
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs7332384; hg19: chr13-27373154;