chr2-59885607-A-C

Variant names:

• chr2-59885607-A-C
• rs17400149
• ENST00000606382.1:n.111-58336T>G

Variant summary

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

The ENST00000650011.1(ENSG00000233891):​n.274-27043T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,958 control chromosomes in the GnomAD database, including 5,841 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 (5841 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000650011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219
• Publications: 4 publications found

Genes affected

ENSG00000233891 (HGNC:58936):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650011.1. 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
	ENSG00000233891	ENST00000606382.1	TSL:5	n.111-58336T>G		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.274-27043T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41947 AN: 151840 Hom.: 5840 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.276 AC: 41965 AN: 151958 Hom.: 5841 Cov.: 32 AF XY: 0.274 AC XY: 20329 AN XY: 74260

African (AFR) AF: 0.276 AC: 11412 AN: 41402

American (AMR) AF: 0.268 AC: 4095 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 991 AN: 3466

East Asian (EAS) AF: 0.212 AC: 1092 AN: 5162

South Asian (SAS) AF: 0.256 AC: 1237 AN: 4824

European-Finnish (FIN) AF: 0.281 AC: 2964 AN: 10540

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19180 AN: 67974

Other (OTH) AF: 0.287 AC: 604 AN: 2104

Alfa AF: 0.281 Hom.: 7939

Bravo AF: 0.277

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.78
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs17400149; hg19: chr2-60112742;