ENST00000781414.1:n.116-11463A>T

Variant names:

• chr2-221811794-A-T
• rs10498122
• ENST00000781414.1:n.116-11463A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000781414.1(ENSG00000301760):​n.116-11463A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 152,234 control chromosomes in the GnomAD database, including 107 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 0.031 (107 hom., cov: 32)
• Consequence: ENSG00000301760 ENST00000781414.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 2 publications found

Genes affected

ENSG00000301760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0307 (4674/152234) while in subpopulation NFE AF = 0.0485 (3298/68010). AF 95% confidence interval is 0.0471. There are 107 homozygotes in GnomAd4. There are 2246 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 107 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301760	ENST00000781414.1	n.116-11463A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0307 AC: 4676 AN: 152116 Hom.: 107 Cov.: 32

Gnomad AFR AF: 0.00792

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0213

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0291

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

GnomAD4 genome AF: 0.0307 AC: 4674 AN: 152234 Hom.: 107 Cov.: 32 AF XY: 0.0302 AC XY: 2246 AN XY: 74446

African (AFR) AF: 0.00789 AC: 328 AN: 41556

American (AMR) AF: 0.0203 AC: 310 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0213 AC: 74 AN: 3470

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0346 AC: 167 AN: 4826

European-Finnish (FIN) AF: 0.0404 AC: 429 AN: 10606

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0485 AC: 3298 AN: 68010

Other (OTH) AF: 0.0284 AC: 60 AN: 2116

Alfa AF: 0.0441 Hom.: 29

Bravo AF: 0.0262

Asia WGS AF: 0.0100 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		0.044

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10498122; hg19: chr2-222676514;