rs1382387

chr16-80072464-C-Achr16-80072464-C-Gchr16-80072464-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000563397.1(ENSG00000260706):n.392+2951C>A variant causes a intron, non coding transcript 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: ENST00000563397.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105371357	XR_001752272.2	n.463+2951C>A		intron_variant, non_coding_transcript_variant
LOC105371357	XR_933774.3	n.392+2951C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563397.1	n.392+2951C>A		intron_variant, non_coding_transcript_variant		4
	ENST00000567851.5	n.405+2951C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.655

Alfa AF: 0.608 Hom.: 3703

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1382387; hg19: chr16-80106361;