rs2397442

Variant names:

• chr16-55275348-G-A
• rs2397442
• ENST00000558730.2:n.215+7190C>T

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.215+7190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,478 control chromosomes in the GnomAD database, including 15,314 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 0.44 (15314 hom., cov: 29)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 1 publications found

Genes affected

ENSG00000259283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558730.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259283	ENST00000558730.2	TSL:3	n.215+7190C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 65970 AN: 151358 Hom.: 15307 Cov.: 29

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.436 AC: 65995 AN: 151478 Hom.: 15314 Cov.: 29 AF XY: 0.439 AC XY: 32473 AN XY: 73960

African (AFR) AF: 0.250 AC: 10306 AN: 41288

American (AMR) AF: 0.513 AC: 7806 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1499 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2524 AN: 5104

South Asian (SAS) AF: 0.518 AC: 2487 AN: 4798

European-Finnish (FIN) AF: 0.479 AC: 5008 AN: 10460

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34918 AN: 67850

Other (OTH) AF: 0.436 AC: 918 AN: 2104

Alfa AF: 0.487 Hom.: 10040

Bravo AF: 0.427

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.81
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2397442; hg19: chr16-55309260;