rs17202778

Positions:

• chr2-207370062-T-C

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, non coding transcript 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: ENST00000412387.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000412387.5	n.261-37367A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000418850.1	n.401-37367A>G		intron_variant, non_coding_transcript_variant		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;