2-214593909-T-C

Variant names:

• chr2-214593909-T-C
• rs7425848
• ENST00000412896.5:n.177+89173A>G

Variant summary

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

The ENST00000412896.5(ENSG00000197585):​n.177+89173A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 151,978 control chromosomes in the GnomAD database, including 46,296 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 0.77 (46296 hom., cov: 30)
• Consequence: ENSG00000197585 ENST00000412896.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 5 publications found

Genes affected

ENSG00000197585 (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 (NFE) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000197585	ENST00000412896.5	n.177+89173A>G		intron_variant	Intron 2 of 3	4
ENSG00000197585	ENST00000437883.1	n.132+90206A>G		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116981 AN: 151860 Hom.: 46284 Cov.: 30

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.770 AC: 117041 AN: 151978 Hom.: 46296 Cov.: 30 AF XY: 0.772 AC XY: 57374 AN XY: 74300

African (AFR) AF: 0.564 AC: 23361 AN: 41390

American (AMR) AF: 0.833 AC: 12712 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2876 AN: 3470

East Asian (EAS) AF: 0.803 AC: 4161 AN: 5180

South Asian (SAS) AF: 0.844 AC: 4037 AN: 4786

European-Finnish (FIN) AF: 0.854 AC: 9042 AN: 10586

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58160 AN: 67984

Other (OTH) AF: 0.788 AC: 1667 AN: 2116

Alfa AF: 0.811 Hom.: 8547

Bravo AF: 0.757

Asia WGS AF: 0.810 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7425848; hg19: chr2-215458633;