rs2788113

Variant names:

• chr9-82198738-G-C
• rs2788113
• ENST00000637606.1:n.256-74669G>C

Variant summary

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

The ENST00000730992.1(ENSG00000290551):​n.119+30964G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 152,102 control chromosomes in the GnomAD database, including 20,169 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 0.47 (20169 hom., cov: 32)
• Consequence: ENSG00000290551 ENST00000730992.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 1 publications found

Genes affected

ENSG00000290551 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730992.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290551	ENST00000637606.1	TSL:5	n.256-74669G>C		intron	N/A
	ENSG00000290551	ENST00000730992.1		n.119+30964G>C		intron	N/A
	ENSG00000290551	ENST00000730993.1		n.57+30964G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71177 AN: 151984 Hom.: 20105 Cov.: 32

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.469 AC: 71300 AN: 152102 Hom.: 20169 Cov.: 32 AF XY: 0.461 AC XY: 34259 AN XY: 74338

African (AFR) AF: 0.801 AC: 33232 AN: 41502

American (AMR) AF: 0.412 AC: 6293 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2630 AN: 5154

South Asian (SAS) AF: 0.307 AC: 1484 AN: 4830

European-Finnish (FIN) AF: 0.238 AC: 2520 AN: 10588

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22383 AN: 67970

Other (OTH) AF: 0.467 AC: 986 AN: 2110

Alfa AF: 0.404 Hom.: 1879

Bravo AF: 0.502

Asia WGS AF: 0.472 AC: 1639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.45
PhyloP100		0.023

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: rs2788113;

hg19: chr9-84813653;