rs2727789

Variant names:

• chr11-116826171-G-T
• rs2727789
• ENST00000814126.1:n.136-1994G>T

Variant summary

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

The ENST00000814126.1(ENSG00000305923):​n.136-1994G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,106 control chromosomes in the GnomAD database, including 22,755 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 0.53 (22755 hom., cov: 33)
• Consequence: ENSG00000305923 ENST00000814126.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 6 publications found

Genes affected

ENSG00000305923 (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 = 0.626 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
ENSG00000305923	ENST00000814126.1	n.136-1994G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80727 AN: 151988 Hom.: 22754 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.531 AC: 80750 AN: 152106 Hom.: 22755 Cov.: 33 AF XY: 0.526 AC XY: 39109 AN XY: 74340

African (AFR) AF: 0.325 AC: 13482 AN: 41488

American (AMR) AF: 0.571 AC: 8724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1942 AN: 3472

East Asian (EAS) AF: 0.614 AC: 3180 AN: 5176

South Asian (SAS) AF: 0.496 AC: 2391 AN: 4824

European-Finnish (FIN) AF: 0.587 AC: 6216 AN: 10590

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42858 AN: 67956

Other (OTH) AF: 0.557 AC: 1172 AN: 2106

Alfa AF: 0.565 Hom.: 3573

Bravo AF: 0.529

Asia WGS AF: 0.540 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.39
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2727789; hg19: chr11-116696887;