2-239723213-T-G

Variant names:

• chr2-239723213-T-G
• rs11891511
• ENST00000771078.1:n.589-3185T>G

Variant summary

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

The ENST00000771078.1(ENSG00000300336):​n.589-3185T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,148 control chromosomes in the GnomAD database, including 3,720 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 0.22 (3720 hom., cov: 33)
• Consequence: ENSG00000300336 ENST00000771078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 2 publications found

Genes affected

ENSG00000300336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771078.1. 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
	ENSG00000300336	ENST00000771078.1		n.589-3185T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32915 AN: 152028 Hom.: 3720 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.216 AC: 32935 AN: 152148 Hom.: 3720 Cov.: 33 AF XY: 0.214 AC XY: 15950 AN XY: 74374

African (AFR) AF: 0.276 AC: 11462 AN: 41508

American (AMR) AF: 0.160 AC: 2442 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3468

East Asian (EAS) AF: 0.270 AC: 1391 AN: 5158

South Asian (SAS) AF: 0.193 AC: 932 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1854 AN: 10600

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13313 AN: 67988

Other (OTH) AF: 0.216 AC: 454 AN: 2106

Alfa AF: 0.200 Hom.: 10952

Bravo AF: 0.217

Asia WGS AF: 0.233 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.91
DANN	Benign	0.47
PhyloP100		-1.5

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: rs11891511;

hg19: chr2-240644907;

COSMIC: COSV51177348;