8-63440471-A-G

Variant names:

• chr8-63440471-A-G
• rs4737649
• ENST00000519819.5:n.72+21008T>C

Variant summary

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

The ENST00000519819.5(ENSG00000253205):​n.72+21008T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,690 control chromosomes in the GnomAD database, including 45,302 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 0.77 (45302 hom., cov: 31)
• Consequence: ENSG00000253205 ENST00000519819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 3 publications found

Genes affected

ENSG00000253205 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519819.5. 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
	ENSG00000253205	ENST00000519819.5	TSL:3	n.72+21008T>C		intron	N/A
	ENSG00000253205	ENST00000521061.1	TSL:4	n.289-6462T>C		intron	N/A
	ENSG00000253205	ENST00000522265.6	TSL:4	n.286+21008T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116429 AN: 151572 Hom.: 45248 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.893

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.768 AC: 116543 AN: 151690 Hom.: 45302 Cov.: 31 AF XY: 0.771 AC XY: 57127 AN XY: 74106

African (AFR) AF: 0.872 AC: 36144 AN: 41470

American (AMR) AF: 0.815 AC: 12384 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2292 AN: 3464

East Asian (EAS) AF: 0.938 AC: 4778 AN: 5096

South Asian (SAS) AF: 0.893 AC: 4305 AN: 4822

European-Finnish (FIN) AF: 0.670 AC: 7072 AN: 10558

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47095 AN: 67770

Other (OTH) AF: 0.770 AC: 1618 AN: 2102

Alfa AF: 0.699 Hom.: 3002

Bravo AF: 0.784

Asia WGS AF: 0.900 AC: 3126 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.62
DANN	Benign	0.52
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs4737649; hg19: chr8-64353029;