chr2-207370062-T-C

Variant names:

• chr2-207370062-T-C
• rs17202778
• ENST00000412387.5:n.261-37367A>G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412387.5(ENSG00000223725):​n.261-37367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,142 control chromosomes in the GnomAD database, including 2,177 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 0.15 (2177 hom., cov: 32)
• Consequence: ENSG00000223725 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

Genes affected

ENSG00000223725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 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
ENSG00000223725	ENST00000412387.5	n.261-37367A>G		intron_variant	Intron 3 of 4	4
ENSG00000223725	ENST00000418850.1	n.401-37367A>G		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22708 AN: 152024 Hom.: 2175 Cov.: 32

Gnomad AFR AF: 0.0340

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.149 AC: 22703 AN: 152142 Hom.: 2177 Cov.: 32 AF XY: 0.152 AC XY: 11340 AN XY: 74370

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.166

Alfa AF: 0.155 Hom.: 305

Bravo AF: 0.136

Asia WGS AF: 0.247 AC: 857 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17202778; hg19: chr2-208234786;