rs798443

Variant names:

• chr2-7828144-G-A
• rs798443
• ENST00000815071.1:n.300+212C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-7828144-G-A
• chr2-7828144-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000815071.1(ENSG00000226506):​n.300+212C>T variant causes a intron change. The variant allele was found at a frequency of 0.614 in 151,978 control chromosomes in the GnomAD database, including 34,578 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 0.61 (34578 hom., cov: 31)
• Consequence: ENSG00000226506 ENST00000815071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.18
• Publications: 17 publications found

Genes affected

ENSG00000226506 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373408	XR_922750.1	n.274+212C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226506	ENST00000815071.1	n.300+212C>T		intron_variant	Intron 2 of 3
ENSG00000226506	ENST00000815072.1	n.518+212C>T		intron_variant	Intron 3 of 3
ENSG00000226506	ENST00000815073.1	n.332+212C>T		intron_variant	Intron 2 of 2
ENSG00000226506	ENST00000815074.1	n.368+212C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93339 AN: 151858 Hom.: 34568 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.614 AC: 93355 AN: 151978 Hom.: 34578 Cov.: 31 AF XY: 0.618 AC XY: 45917 AN XY: 74292

African (AFR) AF: 0.175 AC: 7231 AN: 41382

American (AMR) AF: 0.699 AC: 10665 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2770 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3183 AN: 5168

South Asian (SAS) AF: 0.680 AC: 3266 AN: 4806

European-Finnish (FIN) AF: 0.859 AC: 9090 AN: 10588

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54844 AN: 67980

Other (OTH) AF: 0.621 AC: 1309 AN: 2108

Alfa AF: 0.734 Hom.: 141516

Bravo AF: 0.582

Asia WGS AF: 0.642 AC: 2231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	15
DANN	Benign	0.51
PhyloP100		6.2

Splicing

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

Other links and lift over

dbSNP: rs798443; hg19: chr2-7968275;