rs2788113

chr9-82198738-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637606.1(ENSG00000290551):n.256-74669G>C variant causes a intron, non coding transcript 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: ENST00000637606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105376107	XR_002956914.2	n.625-74669G>C		intron_variant, non_coding_transcript_variant
LOC105376107	XR_002956913.1	n.61+30964G>C		intron_variant, non_coding_transcript_variant
LOC105376107	XR_002956915.2	n.61+30964G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000637606.1	n.256-74669G>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.467

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2788113; hg19: chr9-84813653;