rs4671826

chr2-67681817-C-T

Variant summary

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

The ENST00000419809.1(ENSG00000235495):n.126+2135G>A 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 0.446 in 151,880 control chromosomes in the GnomAD database, including 15,955 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 0.45 (15955 hom., cov: 31)
• Consequence: ENST00000419809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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
	ENST00000419809.1	n.126+2135G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67718 AN: 151762 Hom.: 15942 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.446 AC: 67762 AN: 151880 Hom.: 15955 Cov.: 31 AF XY: 0.445 AC XY: 33041 AN XY: 74208

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.457

Alfa AF: 0.494 Hom.: 9126

Bravo AF: 0.445

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.7
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4671826; hg19: chr2-67908949;