rs6480902

Variant names:

• chr10-78727555-G-A
• rs6480902
• ENST00000764443.1:n.444+16543C>T

Variant summary

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

The ENST00000764443.1(ENSG00000228683):​n.444+16543C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,044 control chromosomes in the GnomAD database, including 22,426 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 0.53 (22426 hom., cov: 31)
• Consequence: ENSG00000228683 ENST00000764443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 2 publications found

Genes affected

ENSG00000228683 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378379	XR_946100.2	n.446+16543C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228683	ENST00000764443.1	n.444+16543C>T		intron_variant	Intron 1 of 3
ENSG00000228683	ENST00000764444.1	n.425+16543C>T		intron_variant	Intron 1 of 2
ENSG00000228683	ENST00000764445.1	n.76+16543C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80697 AN: 151926 Hom.: 22434 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.531 AC: 80706 AN: 152044 Hom.: 22426 Cov.: 31 AF XY: 0.531 AC XY: 39474 AN XY: 74328

African (AFR) AF: 0.370 AC: 15340 AN: 41458

American (AMR) AF: 0.617 AC: 9432 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1579 AN: 5164

South Asian (SAS) AF: 0.512 AC: 2462 AN: 4806

European-Finnish (FIN) AF: 0.624 AC: 6606 AN: 10582

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40975 AN: 67972

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.592 Hom.: 46552

Bravo AF: 0.528

Asia WGS AF: 0.415 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.1
DANN	Benign	0.54
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6480902; hg19: chr10-80487312;