chr2-101990064-G-A

Variant names:

• chr2-101990064-G-A
• rs4141134
• ENST00000723268.1:n.194+649C>T

Variant summary

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

The ENST00000723268.1(ENSG00000294382):​n.194+649C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,124 control chromosomes in the GnomAD database, including 36,175 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 0.68 (36175 hom., cov: 31)
• Consequence: ENSG00000294382 ENST00000723268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 31 publications found

Genes affected

ENSG00000294382 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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
ENSG00000294382	ENST00000723268.1	n.194+649C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102847 AN: 152006 Hom.: 36117 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.677 AC: 102962 AN: 152124 Hom.: 36175 Cov.: 31 AF XY: 0.686 AC XY: 51020 AN XY: 74372

African (AFR) AF: 0.835 AC: 34649 AN: 41500

American (AMR) AF: 0.682 AC: 10424 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1833 AN: 3468

East Asian (EAS) AF: 0.952 AC: 4925 AN: 5172

South Asian (SAS) AF: 0.680 AC: 3283 AN: 4826

European-Finnish (FIN) AF: 0.752 AC: 7970 AN: 10598

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37951 AN: 67964

Other (OTH) AF: 0.650 AC: 1373 AN: 2112

Alfa AF: 0.599 Hom.: 24852

Bravo AF: 0.681

Asia WGS AF: 0.834 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.044
DANN	Benign	0.61
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4141134; hg19: chr2-102606526;