ENST00000797583.1:n.122-26146C>G

Variant names:

• chr5-30931732-G-C
• rs11957363
• ENST00000797583.1:n.122-26146C>G

Variant summary

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

The ENST00000797583.1(ENSG00000303861):​n.122-26146C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,958 control chromosomes in the GnomAD database, including 7,066 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 0.29 (7066 hom., cov: 32)
• Consequence: ENSG00000303861 ENST00000797583.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 0 publications found

Genes affected

ENSG00000303861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 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
ENSG00000303861	ENST00000797583.1	n.122-26146C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44645 AN: 151838 Hom.: 7062 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.294 AC: 44651 AN: 151958 Hom.: 7066 Cov.: 32 AF XY: 0.294 AC XY: 21844 AN XY: 74248

African (AFR) AF: 0.187 AC: 7747 AN: 41470

American (AMR) AF: 0.296 AC: 4517 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1067 AN: 3466

East Asian (EAS) AF: 0.242 AC: 1240 AN: 5126

South Asian (SAS) AF: 0.261 AC: 1257 AN: 4812

European-Finnish (FIN) AF: 0.376 AC: 3970 AN: 10570

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23693 AN: 67932

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.198 Hom.: 459

Bravo AF: 0.281

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.29
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11957363; hg19: chr5-30931839; COSMIC: COSV50955383;