5-69234483-T-C

Variant names:

• chr5-69234483-T-C
• rs2932778
• ENST00000835232.1:n.213+165A>G

Variant summary

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

The ENST00000835232.1(ENSG00000308592):​n.213+165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,890 control chromosomes in the GnomAD database, including 12,798 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 0.41 (12798 hom., cov: 32)
• Consequence: ENSG00000308592 ENST00000835232.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 9 publications found

Genes affected

ENSG00000308592 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 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
ENSG00000308592	ENST00000835232.1	n.213+165A>G		intron_variant	Intron 1 of 2
ENSG00000308592	ENST00000835233.1	n.159+165A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62022 AN: 151772 Hom.: 12784 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.409 AC: 62071 AN: 151890 Hom.: 12798 Cov.: 32 AF XY: 0.413 AC XY: 30622 AN XY: 74222

African (AFR) AF: 0.367 AC: 15214 AN: 41402

American (AMR) AF: 0.444 AC: 6767 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2366 AN: 5162

South Asian (SAS) AF: 0.559 AC: 2695 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4095 AN: 10522

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.414 AC: 28104 AN: 67958

Other (OTH) AF: 0.402 AC: 846 AN: 2104

Alfa AF: 0.409 Hom.: 15695

Bravo AF: 0.406

Asia WGS AF: 0.522 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		0.20
PromoterAI		-0.010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2932778; hg19: chr5-68530310; COSMIC: COSV56507812;