5-33121891-C-G

Variant names:

• chr5-33121891-C-G
• rs1981968
• ENST00000510327.2:n.503-98564G>C

Variant summary

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

The ENST00000510327.2(ENSG00000250697):​n.503-98564G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,092 control chromosomes in the GnomAD database, including 24,697 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 0.55 (24697 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000510327.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217
• Publications: 3 publications found

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510327.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250697	ENST00000510327.2	TSL:3	n.503-98564G>C		intron	N/A
	ENSG00000250697	ENST00000657441.1		n.270-98564G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84270 AN: 151974 Hom.: 24646 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.555 AC: 84381 AN: 152092 Hom.: 24697 Cov.: 32 AF XY: 0.551 AC XY: 40927 AN XY: 74330

African (AFR) AF: 0.752 AC: 31203 AN: 41500

American (AMR) AF: 0.480 AC: 7342 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3470

East Asian (EAS) AF: 0.527 AC: 2724 AN: 5164

South Asian (SAS) AF: 0.456 AC: 2198 AN: 4822

European-Finnish (FIN) AF: 0.452 AC: 4767 AN: 10556

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32653 AN: 67972

Other (OTH) AF: 0.541 AC: 1142 AN: 2110

Alfa AF: 0.518 Hom.: 2616

Bravo AF: 0.568

Asia WGS AF: 0.499 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1981968; hg19: chr5-33121997;