ENST00000751816.1:n.108-27333C>T

Variant names:

• chr1-159699194-C-T
• rs11265257
• ENST00000751816.1:n.108-27333C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-27333C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,884 control chromosomes in the GnomAD database, including 9,830 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 0.35 (9830 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 12 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

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
ENSG00000297913	ENST00000751816.1	n.108-27333C>T		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-27333C>T		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-27333C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52624 AN: 151766 Hom.: 9826 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.347 AC: 52645 AN: 151884 Hom.: 9830 Cov.: 31 AF XY: 0.349 AC XY: 25872 AN XY: 74178

African (AFR) AF: 0.210 AC: 8682 AN: 41430

American (AMR) AF: 0.407 AC: 6209 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1325 AN: 3464

East Asian (EAS) AF: 0.579 AC: 2989 AN: 5164

South Asian (SAS) AF: 0.340 AC: 1637 AN: 4812

European-Finnish (FIN) AF: 0.390 AC: 4088 AN: 10474

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.389 AC: 26424 AN: 67960

Other (OTH) AF: 0.364 AC: 767 AN: 2110

Alfa AF: 0.298 Hom.: 1817

Bravo AF: 0.341

Asia WGS AF: 0.442 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.040
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11265257; hg19: chr1-159668984;