16-60472623-C-T

Variant names:

• chr16-60472623-C-T
• rs2042389
• ENST00000659433.2:n.299-113C>T

Variant summary

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

The ENST00000659433.2(ENSG00000261436):​n.299-113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 151,992 control chromosomes in the GnomAD database, including 5,735 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 0.27 (5735 hom., cov: 32)
• Consequence: ENSG00000261436 ENST00000659433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927605	XR_001752229.1	n.539-113C>T		intron_variant	Intron 4 of 6
LOC101927605	XR_001752230.1	n.516-113C>T		intron_variant	Intron 4 of 6
LOC101927605	XR_001752231.1	n.313-113C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261436	ENST00000659433.2	n.299-113C>T		intron_variant	Intron 3 of 5
ENSG00000261436	ENST00000660937.2	n.525-113C>T		intron_variant	Intron 5 of 6
ENSG00000261436	ENST00000661470.1	n.368-113C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40964 AN: 151876 Hom.: 5726 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.270 AC: 41003 AN: 151992 Hom.: 5735 Cov.: 32 AF XY: 0.270 AC XY: 20023 AN XY: 74286

African (AFR) AF: 0.251 AC: 10390 AN: 41448

American (AMR) AF: 0.274 AC: 4197 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3468

East Asian (EAS) AF: 0.462 AC: 2377 AN: 5146

South Asian (SAS) AF: 0.248 AC: 1194 AN: 4822

European-Finnish (FIN) AF: 0.223 AC: 2356 AN: 10550

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18219 AN: 67956

Other (OTH) AF: 0.303 AC: 639 AN: 2106

Alfa AF: 0.272 Hom.: 1151

Bravo AF: 0.279

Asia WGS AF: 0.373 AC: 1292 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.41
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2042389; hg19: chr16-60506527;