5-74993244-T-C

Variant names:

• chr5-74993244-T-C
• rs6453104
• ENST00000505200.1:n.213-5621A>G

Variant summary

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

The ENST00000505200.1(ENSG00000249856):​n.213-5621A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,072 control chromosomes in the GnomAD database, including 20,910 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 0.50 (20910 hom., cov: 32)
• Consequence: ENSG00000249856 ENST00000505200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911
• Publications: 8 publications found

Genes affected

ENSG00000249856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 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
ENSG00000249856	ENST00000505200.1	n.213-5621A>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76084 AN: 151954 Hom.: 20864 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.501 AC: 76194 AN: 152072 Hom.: 20910 Cov.: 32 AF XY: 0.498 AC XY: 37018 AN XY: 74350

African (AFR) AF: 0.753 AC: 31250 AN: 41500

American (AMR) AF: 0.426 AC: 6506 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1403 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1969 AN: 5174

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4812

European-Finnish (FIN) AF: 0.422 AC: 4453 AN: 10556

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27248 AN: 67978

Other (OTH) AF: 0.460 AC: 972 AN: 2114

Alfa AF: 0.427 Hom.: 60834

Bravo AF: 0.515

Asia WGS AF: 0.410 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.44
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs6453104; hg19: chr5-74289069;