rs17325209

chr2-48252071-G-Achr2-48252071-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651429.1(ENSG00000230773):n.168+61619C>T 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 0.0812 in 151,946 control chromosomes in the GnomAD database, including 696 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 0.081 (696 hom., cov: 31)
• Consequence: ENST00000651429.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 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
	ENST00000651429.1	n.168+61619C>T		intron_variant, non_coding_transcript_variant
	ENST00000650704.1	n.140-8452C>T		intron_variant, non_coding_transcript_variant
	ENST00000658896.1	n.186+61619C>T		intron_variant, non_coding_transcript_variant
	ENST00000661667.2	n.168-8452C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0813 AC: 12341 AN: 151830 Hom.: 696 Cov.: 31

Gnomad AFR AF: 0.0281

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0564

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0812 AC: 12341 AN: 151946 Hom.: 696 Cov.: 31 AF XY: 0.0794 AC XY: 5893 AN XY: 74254

Gnomad4 AFR AF: 0.0280

Gnomad4 AMR AF: 0.0563

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0790

Alfa AF: 0.0690 Hom.: 122

Bravo AF: 0.0733

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.0
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17325209; hg19: chr2-48479210;