rs1372878

Variant names:

• chr2-59677430-G-A
• rs1372878
• ENST00000412409.3:n.261+42146C>T

Variant summary

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

The ENST00000412409.3(ENSG00000233891):​n.261+42146C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,202 control chromosomes in the GnomAD database, including 606 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 0.063 (606 hom., cov: 32)
• Consequence: ENSG00000233891 ENST00000412409.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 3 publications found

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412409.3. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233891	ENST00000412409.3	TSL:3	n.261+42146C>T		intron	N/A
	ENSG00000233891	ENST00000435557.1	TSL:4	n.224-7882C>T		intron	N/A
	ENSG00000233891	ENST00000606382.1	TSL:5	n.236+149716C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0633 AC: 9621 AN: 152084 Hom.: 605 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.0903

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0633 AC: 9635 AN: 152202 Hom.: 606 Cov.: 32 AF XY: 0.0653 AC XY: 4860 AN XY: 74420

African (AFR) AF: 0.0873 AC: 3625 AN: 41528

American (AMR) AF: 0.0619 AC: 946 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3470

East Asian (EAS) AF: 0.361 AC: 1865 AN: 5170

South Asian (SAS) AF: 0.0899 AC: 433 AN: 4814

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10618

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0338 AC: 2296 AN: 68010

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0458 Hom.: 722

Bravo AF: 0.0679

Asia WGS AF: 0.173 AC: 599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1372878; hg19: chr2-59904565;