rs2202749

Variant names:

• chr8-80362103-A-G
• rs2202749
• ENST00000644465.1:n.253+73101A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-80362103-A-G
• chr8-80362103-A-T

Variant summary

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

The ENST00000644465.1(ENSG00000253238):​n.253+73101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 150,240 control chromosomes in the GnomAD database, including 28,538 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 (28538 hom., cov: 26)
• Consequence: ENSG00000253238 ENST00000644465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 7 publications found

Genes affected

ENSG00000253238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644465.1. 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
	ENSG00000253238	ENST00000644465.1		n.253+73101A>G		intron	N/A
	ENSG00000253238	ENST00000656157.2		n.285+73101A>G		intron	N/A
	ENSG00000253238	ENST00000656811.1		n.252-40633A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 91970 AN: 150132 Hom.: 28525 Cov.: 26

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.612 AC: 92021 AN: 150240 Hom.: 28538 Cov.: 26 AF XY: 0.611 AC XY: 44658 AN XY: 73148

African (AFR) AF: 0.585 AC: 23818 AN: 40698

American (AMR) AF: 0.564 AC: 8493 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2056 AN: 3464

East Asian (EAS) AF: 0.395 AC: 2019 AN: 5116

South Asian (SAS) AF: 0.547 AC: 2599 AN: 4750

European-Finnish (FIN) AF: 0.686 AC: 6936 AN: 10118

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.647 AC: 43852 AN: 67746

Other (OTH) AF: 0.621 AC: 1305 AN: 2100

Alfa AF: 0.620 Hom.: 3506

Bravo AF: 0.597

Asia WGS AF: 0.518 AC: 1797 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.23
PhyloP100		-0.79

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: rs2202749;

hg19: chr8-81274338;