2-103872893-C-T

Variant names:

• chr2-103872893-C-T
• rs3860446
• ENST00000455716.2:n.198+7119G>A

Variant summary

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

The ENST00000455716.2(ENSG00000236141):​n.198+7119G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,036 control chromosomes in the GnomAD database, including 26,534 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 0.54 (26534 hom., cov: 32)
• Consequence: ENSG00000236141 ENST00000455716.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 7 publications found

Genes affected

ENSG00000236141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 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
ENSG00000236141	ENST00000455716.2	n.198+7119G>A		intron_variant	Intron 1 of 2	4
ENSG00000236141	ENST00000777272.1	n.159+7119G>A		intron_variant	Intron 1 of 4
ENSG00000236141	ENST00000777273.1	n.158+7119G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81217 AN: 151918 Hom.: 26469 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.535 AC: 81344 AN: 152036 Hom.: 26534 Cov.: 32 AF XY: 0.545 AC XY: 40468 AN XY: 74312

African (AFR) AF: 0.865 AC: 35875 AN: 41472

American (AMR) AF: 0.547 AC: 8353 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3468

East Asian (EAS) AF: 0.992 AC: 5133 AN: 5174

South Asian (SAS) AF: 0.649 AC: 3124 AN: 4810

European-Finnish (FIN) AF: 0.412 AC: 4349 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21930 AN: 67960

Other (OTH) AF: 0.483 AC: 1019 AN: 2110

Alfa AF: 0.387 Hom.: 21038

Bravo AF: 0.558

Asia WGS AF: 0.831 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs3860446; hg19: chr2-104489351;