ENST00000796160.1:n.277+1889C>T

Variant names:

• chr11-115137885-G-A
• rs2507905
• ENST00000796160.1:n.277+1889C>T

Variant summary

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

The ENST00000796160.1(ENSG00000303624):​n.277+1889C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,110 control chromosomes in the GnomAD database, including 3,718 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 0.20 (3718 hom., cov: 32)
• Consequence: ENSG00000303624 ENST00000796160.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 3 publications found

Genes affected

ENSG00000303624 (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 (SAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796160.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303624	ENST00000796160.1		n.277+1889C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30248 AN: 151994 Hom.: 3710 Cov.: 32

Gnomad AFR AF: 0.0699

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.199 AC: 30260 AN: 152110 Hom.: 3718 Cov.: 32 AF XY: 0.203 AC XY: 15126 AN XY: 74352

African (AFR) AF: 0.0697 AC: 2895 AN: 41514

American (AMR) AF: 0.247 AC: 3774 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.128 AC: 663 AN: 5168

South Asian (SAS) AF: 0.382 AC: 1840 AN: 4818

European-Finnish (FIN) AF: 0.288 AC: 3035 AN: 10554

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16983 AN: 67988

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.212 Hom.: 598

Bravo AF: 0.185

Asia WGS AF: 0.238 AC: 830 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	1.6
DANN	Benign	0.35
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2507905; hg19: chr11-115008605;