5-36398275-A-G

Variant names:

• chr5-36398275-A-G
• rs2967072
• ENST00000797344.1:n.250+25344T>C

Variant summary

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

The ENST00000797344.1(ENSG00000303823):​n.250+25344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0533 in 152,220 control chromosomes in the GnomAD database, including 360 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 0.053 (360 hom., cov: 32)
• Consequence: ENSG00000303823 ENST00000797344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 0 publications found

Genes affected

ENSG00000303823 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797344.1. 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
	ENSG00000303823	ENST00000797344.1		n.250+25344T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0533 AC: 8104 AN: 152102 Hom.: 358 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0533 AC: 8119 AN: 152220 Hom.: 360 Cov.: 32 AF XY: 0.0587 AC XY: 4365 AN XY: 74410

African (AFR) AF: 0.0533 AC: 2213 AN: 41544

American (AMR) AF: 0.0200 AC: 306 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3472

East Asian (EAS) AF: 0.156 AC: 807 AN: 5166

South Asian (SAS) AF: 0.214 AC: 1032 AN: 4820

European-Finnish (FIN) AF: 0.100 AC: 1064 AN: 10592

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0358 AC: 2433 AN: 68014

Other (OTH) AF: 0.0483 AC: 102 AN: 2112

Alfa AF: 0.0397 Hom.: 309

Bravo AF: 0.0445

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.9
DANN	Benign	0.89
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs2967072; hg19: chr5-36398377;