rs2042389

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659433.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261436	ENST00000659433.2		n.299-113C>T		intron	N/A
	ENSG00000261436	ENST00000660937.2		n.525-113C>T		intron	N/A
	ENSG00000261436	ENST00000661470.1		n.368-113C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2042389;

hg19: chr16-60506527;