chr2-240674832-G-A

Variant names:

• chr2-240674832-G-A
• rs10199388
• ENST00000765066.1:n.137+42G>A

Variant summary

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

The ENST00000765066.1(ENSG00000219159):​n.137+42G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 151,242 control chromosomes in the GnomAD database, including 49,109 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 0.80 (49109 hom., cov: 31)
• Consequence: ENSG00000219159 ENST00000765066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 3 publications found

Genes affected

ENSG00000219159 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765066.1. 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
	ENSG00000219159	ENST00000765066.1		n.137+42G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 121607 AN: 151128 Hom.: 49069 Cov.: 31

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.805 AC: 121690 AN: 151242 Hom.: 49109 Cov.: 31 AF XY: 0.800 AC XY: 59145 AN XY: 73888

African (AFR) AF: 0.835 AC: 34412 AN: 41228

American (AMR) AF: 0.849 AC: 12911 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2834 AN: 3464

East Asian (EAS) AF: 0.640 AC: 3261 AN: 5094

South Asian (SAS) AF: 0.733 AC: 3501 AN: 4774

European-Finnish (FIN) AF: 0.722 AC: 7576 AN: 10488

Middle Eastern (MID) AF: 0.914 AC: 267 AN: 292

European-Non Finnish (NFE) AF: 0.805 AC: 54452 AN: 67676

Other (OTH) AF: 0.827 AC: 1741 AN: 2106

Alfa AF: 0.808 Hom.: 9500

Bravo AF: 0.817

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.61
DANN	Benign	0.52
PhyloP100		-0.25

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: rs10199388;

hg19: chr2-241614249;