2-145331699-T-C

Variant names:

• chr2-145331699-T-C
• rs1822882
• ENST00000454965.1:n.42+107A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454965.1(ENSG00000235435):​n.42+107A>G variant causes a intron 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: ENSG00000235435 ENST00000454965.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 5 publications found

Genes affected

ENSG00000235435 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235435	ENST00000454965.1	n.42+107A>G		intron_variant	Intron 1 of 4	3
ENSG00000309192	ENST00000839437.1	n.54-4239T>C		intron_variant	Intron 1 of 2
ENSG00000309192	ENST00000839438.1	n.54-4239T>C		intron_variant	Intron 1 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.781 AC: 32395 AN: 41462

American (AMR) AF: 0.843 AC: 12864 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3050 AN: 3468

East Asian (EAS) AF: 0.664 AC: 3413 AN: 5140

South Asian (SAS) AF: 0.746 AC: 3598 AN: 4826

European-Finnish (FIN) AF: 0.814 AC: 8614 AN: 10584

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.878 AC: 59665 AN: 67976

Other (OTH) AF: 0.848 AC: 1790 AN: 2112

Alfa AF: 0.867 Hom.: 74698

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1822882; hg19: chr2-146089267;