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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815071.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226506	ENST00000815071.1		n.300+212C>T		intron	N/A
	ENSG00000226506	ENST00000815072.1		n.518+212C>T		intron	N/A
	ENSG00000226506	ENST00000815073.1		n.332+212C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs798443;

hg19: chr2-7968275;