rs4072096

Variant names:

• chr2-226171887-A-C
• rs4072096
• ENST00000719962.1:n.93+13433T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-226171887-A-C
• chr2-226171887-A-T

Variant summary

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

The ENST00000719962.1(ENSG00000235070):​n.93+13433T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,508 control chromosomes in the GnomAD database, including 23,323 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 0.55 (23323 hom., cov: 30)
• Consequence: ENSG00000235070 ENST00000719962.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 10 publications found

Genes affected

ENSG00000235070 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC646736	NR_046102.1	n.505-2860A>C		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235070	ENST00000719962.1	n.93+13433T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.547 AC: 82760 AN: 151390 Hom.: 23280 Cov.: 30

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.547 AC: 82844 AN: 151508 Hom.: 23323 Cov.: 30 AF XY: 0.551 AC XY: 40765 AN XY: 73992

African (AFR) AF: 0.689 AC: 28437 AN: 41288

American (AMR) AF: 0.532 AC: 8108 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3466

East Asian (EAS) AF: 0.536 AC: 2761 AN: 5148

South Asian (SAS) AF: 0.455 AC: 2183 AN: 4800

European-Finnish (FIN) AF: 0.589 AC: 6126 AN: 10406

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32225 AN: 67848

Other (OTH) AF: 0.510 AC: 1074 AN: 2104

Alfa AF: 0.513 Hom.: 3064

Bravo AF: 0.553

Asia WGS AF: 0.426 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.51
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4072096; hg19: chr2-227036603;