ENST00000690790.3:n.305-2225T>C

Variant names:

• chr11-64329761-A-G
• rs694739
• ENST00000690790.3:n.305-2225T>C

Variant summary

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

The ENST00000690790.3(ENSG00000236935):​n.305-2225T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,182 control chromosomes in the GnomAD database, including 7,443 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 0.28 (7443 hom., cov: 33)
• Consequence: ENSG00000236935 ENST00000690790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 101 publications found

Genes affected

ENSG00000236935 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690790.3. 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
	LOC102723878	NR_188518.1		n.432-2225T>C		intron	N/A
	LOC102723878	NR_188519.1		n.1818-2225T>C		intron	N/A
	LOC102723878	NR_188520.1		n.257-2225T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000236935	ENST00000690790.3		n.305-2225T>C		intron	N/A
	ENSG00000236935	ENST00000809504.1		n.611-2225T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42586 AN: 152062 Hom.: 7441 Cov.: 33

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.280 AC: 42595 AN: 152182 Hom.: 7443 Cov.: 33 AF XY: 0.283 AC XY: 21066 AN XY: 74376

African (AFR) AF: 0.0715 AC: 2971 AN: 41550

American (AMR) AF: 0.345 AC: 5274 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3466

East Asian (EAS) AF: 0.169 AC: 875 AN: 5178

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4826

European-Finnish (FIN) AF: 0.410 AC: 4336 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25476 AN: 67992

Other (OTH) AF: 0.264 AC: 558 AN: 2110

Alfa AF: 0.344 Hom.: 34315

Bravo AF: 0.266

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.45
PhyloP100		-1.1

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: rs694739;

hg19: chr11-64097233;