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 ENST00000637606.1(ENSG00000290551):​n.256-74669G>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 ENST00000637606.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376107	XR_002956913.1	n.61+30964G>C		intron_variant	Intron 1 of 4
LOC105376107	XR_002956914.2	n.625-74669G>C		intron_variant	Intron 1 of 4
LOC105376107	XR_002956915.2	n.61+30964G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290551	ENST00000637606.1	n.256-74669G>C		intron_variant	Intron 1 of 9	5
ENSG00000290551	ENST00000730992.1	n.119+30964G>C		intron_variant	Intron 2 of 7
ENSG00000290551	ENST00000730993.1	n.57+30964G>C		intron_variant	Intron 1 of 6

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 v4.3

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

Other links and lift over

dbSNP: rs2788113; hg19: chr9-84813653;