chr5-36541200-C-T

Variant names:

• chr5-36541200-C-T
• rs9292633
• ENST00000751409.1:n.110+11957G>A

Variant summary

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

The ENST00000751409.1(ENSG00000297854):​n.110+11957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,010 control chromosomes in the GnomAD database, including 14,395 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 0.40 (14395 hom., cov: 33)
• Consequence: ENSG00000297854 ENST00000751409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 2 publications found

Genes affected

ENSG00000297854 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751409.1. 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
	ENSG00000297854	ENST00000751409.1		n.110+11957G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60498 AN: 151892 Hom.: 14349 Cov.: 33

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.399 AC: 60604 AN: 152010 Hom.: 14395 Cov.: 33 AF XY: 0.398 AC XY: 29569 AN XY: 74266

African (AFR) AF: 0.670 AC: 27772 AN: 41470

American (AMR) AF: 0.286 AC: 4373 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 830 AN: 3472

East Asian (EAS) AF: 0.133 AC: 687 AN: 5178

South Asian (SAS) AF: 0.197 AC: 947 AN: 4814

European-Finnish (FIN) AF: 0.402 AC: 4235 AN: 10528

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20799 AN: 67958

Other (OTH) AF: 0.360 AC: 762 AN: 2114

Alfa AF: 0.315 Hom.: 13947

Bravo AF: 0.401

Asia WGS AF: 0.214 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.54
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9292633; hg19: chr5-36541302;