chr10-59510907-G-A

Variant names:

• chr10-59510907-G-A
• rs10826304
• ENST00000796729.1:n.106+27807C>T

Variant summary

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

The ENST00000796729.1(ENSG00000303721):​n.106+27807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,026 control chromosomes in the GnomAD database, including 13,317 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 0.40 (13317 hom., cov: 32)
• Consequence: ENSG00000303721 ENST00000796729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376
• Publications: 1 publications found

Genes affected

ENSG00000303721 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984235	XR_001747457.1	n.84+27807C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303721	ENST00000796729.1	n.106+27807C>T		intron_variant	Intron 1 of 3
ENSG00000303721	ENST00000796730.1	n.219+11668C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60263 AN: 151908 Hom.: 13323 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.396 AC: 60260 AN: 152026 Hom.: 13317 Cov.: 32 AF XY: 0.398 AC XY: 29562 AN XY: 74278

African (AFR) AF: 0.194 AC: 8066 AN: 41482

American (AMR) AF: 0.369 AC: 5632 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1858 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2816 AN: 5168

South Asian (SAS) AF: 0.446 AC: 2152 AN: 4828

European-Finnish (FIN) AF: 0.463 AC: 4875 AN: 10520

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33252 AN: 67960

Other (OTH) AF: 0.451 AC: 954 AN: 2116

Alfa AF: 0.333 Hom.: 1457

Bravo AF: 0.380

Asia WGS AF: 0.431 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs10826304; hg19: chr10-61270665; COSMIC: COSV56522401;