16-60394659-G-C

Variant names:

• chr16-60394659-G-C
• rs10500423
• ENST00000565133.1:n.354+29564G>C

Variant summary

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

The ENST00000565133.1(ENSG00000261436):​n.354+29564G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 152,094 control chromosomes in the GnomAD database, including 6,339 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 0.28 (6339 hom., cov: 32)
• Consequence: ENSG00000261436 ENST00000565133.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 1 publications found

Genes affected

ENSG00000261436 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927605	XR_001752229.1	n.538+29564G>C		intron_variant	Intron 4 of 6
LOC101927605	XR_001752230.1	n.515+29564G>C		intron_variant	Intron 4 of 6
LOC101927605	XR_001752231.1	n.312+29564G>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261436	ENST00000565133.1	n.354+29564G>C		intron_variant	Intron 3 of 4	3
ENSG00000261436	ENST00000659433.2	n.298+29564G>C		intron_variant	Intron 3 of 5
ENSG00000261436	ENST00000660937.2	n.469+29564G>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43007 AN: 151976 Hom.: 6337 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.283 AC: 43044 AN: 152094 Hom.: 6339 Cov.: 32 AF XY: 0.280 AC XY: 20836 AN XY: 74360

African (AFR) AF: 0.262 AC: 10861 AN: 41492

American (AMR) AF: 0.205 AC: 3125 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3470

East Asian (EAS) AF: 0.113 AC: 583 AN: 5168

South Asian (SAS) AF: 0.191 AC: 923 AN: 4822

European-Finnish (FIN) AF: 0.359 AC: 3791 AN: 10566

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21830 AN: 67994

Other (OTH) AF: 0.261 AC: 550 AN: 2110

Alfa AF: 0.307 Hom.: 919

Bravo AF: 0.269

Asia WGS AF: 0.136 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.47
DANN	Benign	0.33
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10500423; hg19: chr16-60428563;