chr8-88748082-A-G

Variant names:

• chr8-88748082-A-G
• rs7004633
• ENST00000649573.1:n.141+47733A>G

Variant summary

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

The ENST00000649573.1(ENSG00000253553):​n.141+47733A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,036 control chromosomes in the GnomAD database, including 6,764 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 0.28 (6764 hom., cov: 32)
• Consequence: ENSG00000253553 ENST00000649573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 41 publications found

Genes affected

ENSG00000253553 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375630	XR_001745653.3	n.356-77582A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253553	ENST00000649573.1	n.141+47733A>G		intron_variant	Intron 2 of 7
ENSG00000253553	ENST00000653184.1	n.144+47733A>G		intron_variant	Intron 2 of 6
ENSG00000253553	ENST00000659668.1	n.176+47733A>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41875 AN: 151918 Hom.: 6731 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.276 AC: 41960 AN: 152036 Hom.: 6764 Cov.: 32 AF XY: 0.278 AC XY: 20662 AN XY: 74322

African (AFR) AF: 0.436 AC: 18054 AN: 41434

American (AMR) AF: 0.321 AC: 4899 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 772 AN: 3466

East Asian (EAS) AF: 0.191 AC: 987 AN: 5176

South Asian (SAS) AF: 0.345 AC: 1665 AN: 4832

European-Finnish (FIN) AF: 0.161 AC: 1703 AN: 10586

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12920 AN: 67966

Other (OTH) AF: 0.291 AC: 612 AN: 2104

Alfa AF: 0.215 Hom.: 17305

Bravo AF: 0.293

Asia WGS AF: 0.342 AC: 1186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7004633; hg19: chr8-89760311;