chr2-160244658-G-A

Position:

• chr2-160244658-G-A

Variant summary

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

The ENST00000498478.1(ENSG00000285155):​n.260+8932C>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 0.84 in 152,148 control chromosomes in the GnomAD database, including 53,845 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 0.84 (53845 hom., cov: 31)
• Consequence: ENST00000498478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000498478.1	n.260+8932C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127731 AN: 152030 Hom.: 53790 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.840 AC: 127839 AN: 152148 Hom.: 53845 Cov.: 31 AF XY: 0.841 AC XY: 62588 AN XY: 74380

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.825

Alfa AF: 0.832 Hom.: 14695

Bravo AF: 0.844

Asia WGS AF: 0.863 AC: 2997 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925757; hg19: chr2-161101169;