chr2-236588594-A-G

Variant names:

• chr2-236588594-A-G
• rs11901793
• ENST00000779927.1:n.193+3962A>G

Variant summary

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

The ENST00000779927.1(ENSG00000301575):​n.193+3962A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,092 control chromosomes in the GnomAD database, including 16,919 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 0.37 (16919 hom., cov: 32)
• Consequence: ENSG00000301575 ENST00000779927.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 7 publications found

Genes affected

ENSG00000301575 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779927.1. 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
	ENSG00000301575	ENST00000779927.1		n.193+3962A>G		intron	N/A
	ENSG00000301575	ENST00000779928.1		n.122+3190A>G		intron	N/A
	ENSG00000301575	ENST00000779929.1		n.120+3190A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56780 AN: 151974 Hom.: 16861 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.374 AC: 56886 AN: 152092 Hom.: 16919 Cov.: 32 AF XY: 0.365 AC XY: 27156 AN XY: 74348

African (AFR) AF: 0.832 AC: 34503 AN: 41488

American (AMR) AF: 0.219 AC: 3340 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 706 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1336 AN: 5170

South Asian (SAS) AF: 0.281 AC: 1352 AN: 4806

European-Finnish (FIN) AF: 0.128 AC: 1353 AN: 10600

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13383 AN: 67972

Other (OTH) AF: 0.332 AC: 700 AN: 2108

Alfa AF: 0.250 Hom.: 26240

Bravo AF: 0.400

Asia WGS AF: 0.274 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	16
DANN	Benign	0.75
PhyloP100		0.53

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: rs11901793;

hg19: chr2-237497237;