ENST00000565374.2:n.612+6312T>G

Variant names:

• chr16-82568478-A-C
• rs17244777
• ENST00000565374.2:n.612+6312T>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+6312T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,062 control chromosomes in the GnomAD database, including 5,158 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 0.23 (5158 hom., cov: 32)
• Consequence: ENSG00000261285 ENST00000565374.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928392	NR_188568.1	n.543+6312T>G		intron_variant	Intron 2 of 2
LOC101928392	NR_188569.1	n.543+6312T>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+6312T>G		intron_variant	Intron 2 of 2	3
ENSG00000261285	ENST00000650164.1	n.584+6312T>G		intron_variant	Intron 2 of 5
ENSG00000307474	ENST00000826480.1	n.38+17336A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35497 AN: 151944 Hom.: 5164 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.233 AC: 35484 AN: 152062 Hom.: 5158 Cov.: 32 AF XY: 0.234 AC XY: 17383 AN XY: 74332

African (AFR) AF: 0.0670 AC: 2783 AN: 41518

American (AMR) AF: 0.167 AC: 2557 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.258 AC: 1327 AN: 5150

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4820

European-Finnish (FIN) AF: 0.340 AC: 3598 AN: 10572

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21994 AN: 67942

Other (OTH) AF: 0.205 AC: 431 AN: 2104

Alfa AF: 0.245 Hom.: 989

Bravo AF: 0.210

Asia WGS AF: 0.264 AC: 914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.19
DANN	Benign	0.56
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs17244777; hg19: chr16-82602083;