2-106044245-T-C

Variant names:

• chr2-106044245-T-C
• rs2377445
• ENST00000790593.1:n.640+2679T>C

Variant summary

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

The ENST00000790593.1(ENSG00000302943):​n.640+2679T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,048 control chromosomes in the GnomAD database, including 34,667 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 0.67 (34667 hom., cov: 32)
• Consequence: ENSG00000302943 ENST00000790593.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

ENSG00000302943 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 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
ENSG00000302943	ENST00000790593.1	n.640+2679T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102097 AN: 151930 Hom.: 34655 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.672 AC: 102151 AN: 152048 Hom.: 34667 Cov.: 32 AF XY: 0.672 AC XY: 49960 AN XY: 74312

African (AFR) AF: 0.640 AC: 26520 AN: 41460

American (AMR) AF: 0.626 AC: 9582 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3472

East Asian (EAS) AF: 0.437 AC: 2252 AN: 5150

South Asian (SAS) AF: 0.651 AC: 3136 AN: 4814

European-Finnish (FIN) AF: 0.699 AC: 7388 AN: 10566

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48145 AN: 67972

Other (OTH) AF: 0.696 AC: 1471 AN: 2112

Alfa AF: 0.690 Hom.: 91379

Bravo AF: 0.659

Asia WGS AF: 0.522 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.26
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2377445; hg19: chr2-106660701; COSMIC: COSV60088598;