rs1382387

Variant names:

• chr16-80072464-C-A
• rs1382387
• ENST00000563397.1:n.392+2951C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-80072464-C-A
• chr16-80072464-C-G
• chr16-80072464-C-T

Variant summary

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

The ENST00000563397.1(ENSG00000260706):​n.392+2951C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,078 control chromosomes in the GnomAD database, including 30,522 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 0.62 (30522 hom., cov: 32)
• Consequence: ENSG00000260706 ENST00000563397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77
• Publications: 19 publications found

Genes affected

ENSG00000260706 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371357	XR_001752272.2	n.463+2951C>A		intron_variant	Intron 2 of 2
LOC105371357	XR_933774.3	n.392+2951C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260706	ENST00000563397.1	n.392+2951C>A		intron_variant	Intron 2 of 2	4
ENSG00000260706	ENST00000567851.5	n.405+2951C>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94368 AN: 151960 Hom.: 30517 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.621 AC: 94390 AN: 152078 Hom.: 30522 Cov.: 32 AF XY: 0.627 AC XY: 46584 AN XY: 74354

African (AFR) AF: 0.423 AC: 17558 AN: 41468

American (AMR) AF: 0.706 AC: 10786 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2700 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3521 AN: 5168

South Asian (SAS) AF: 0.694 AC: 3344 AN: 4816

European-Finnish (FIN) AF: 0.743 AC: 7865 AN: 10592

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46489 AN: 67970

Other (OTH) AF: 0.655 AC: 1385 AN: 2116

Alfa AF: 0.580 Hom.: 10507

Bravo AF: 0.611

Asia WGS AF: 0.682 AC: 2370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.7
DANN	Benign	0.68
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs1382387; hg19: chr16-80106361;