rs7186479

Variant names:

• chr16-82569131-T-C
• rs7186479
• ENST00000565374.2:n.612+5659A>G

Variant summary

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

The ENST00000565374.2(ENSG00000261285):​n.612+5659A>G 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 152,210 control chromosomes in the GnomAD database, including 14,764 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 (14764 hom., cov: 33)
• Consequence: ENSG00000261285 ENST00000565374.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.999
• Publications: 5 publications found

Genes affected

ENSG00000261285 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928392	NR_188568.1	n.543+5659A>G		intron_variant	Intron 2 of 2
LOC101928392	NR_188569.1	n.543+5659A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261285	ENST00000565374.2	n.612+5659A>G		intron_variant	Intron 2 of 2	3
ENSG00000261285	ENST00000650164.1	n.584+5659A>G		intron_variant	Intron 2 of 5
ENSG00000307474	ENST00000826480.1	n.38+17989T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61738 AN: 152092 Hom.: 14768 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.406 AC: 61736 AN: 152210 Hom.: 14764 Cov.: 33 AF XY: 0.402 AC XY: 29890 AN XY: 74414

African (AFR) AF: 0.159 AC: 6607 AN: 41546

American (AMR) AF: 0.409 AC: 6257 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5170

South Asian (SAS) AF: 0.400 AC: 1934 AN: 4834

European-Finnish (FIN) AF: 0.495 AC: 5242 AN: 10584

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37356 AN: 67994

Other (OTH) AF: 0.476 AC: 1005 AN: 2112

Alfa AF: 0.504 Hom.: 64126

Bravo AF: 0.391

Asia WGS AF: 0.271 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs7186479; hg19: chr16-82602736;