chr2-145331699-T-C

Position:

• chr2-145331699-T-C

Variant summary

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

The ENST00000454965.1(ENSG00000235435):​n.42+107A>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 0.832 in 152,034 control chromosomes in the GnomAD database, including 52,817 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 0.83 (52816 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: ENST00000454965.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 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
	ENST00000454965.1	n.42+107A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126323 AN: 151914 Hom.: 52765 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.852

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.832 AC: 126432 AN: 152032 Hom.: 52816 Cov.: 32 AF XY: 0.827 AC XY: 61414 AN XY: 74298

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.848

Alfa AF: 0.871 Hom.: 58035

Bravo AF: 0.831

Asia WGS AF: 0.693 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1822882; hg19: chr2-146089267;