2-160203673-A-G

Position:

• chr2-160203673-A-G

Variant summary

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

The ENST00000498478.1(ENSG00000285155):​n.261-2456T>C 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 0.304 in 152,120 control chromosomes in the GnomAD database, including 8,739 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 0.30 (8739 hom., cov: 32)
• Consequence: ENST00000498478.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.415 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
	ENST00000498478.1	n.261-2456T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46246 AN: 152002 Hom.: 8738 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.304 AC: 46251 AN: 152120 Hom.: 8739 Cov.: 32 AF XY: 0.307 AC XY: 22812 AN XY: 74344

Gnomad4 AFR AF: 0.0908

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.286

Alfa AF: 0.359 Hom.: 1378

Bravo AF: 0.281

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4665162; hg19: chr2-161060184;