chr10-48989390-G-T

Variant names:

• chr10-48989390-G-T
• rs7086917
• ENST00000422966.1:n.402+4425G>T

Variant summary

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

The ENST00000422966.1(ENSG00000226576):​n.402+4425G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,954 control chromosomes in the GnomAD database, including 14,657 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 0.43 (14657 hom., cov: 32)
• Consequence: ENSG00000226576 ENST00000422966.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 2 publications found

Genes affected

ENSG00000226576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 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
ENSG00000226576	ENST00000422966.1	n.402+4425G>T		intron_variant	Intron 1 of 1	3
ENSG00000233665	ENST00000428825.8	n.637+3020C>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65393 AN: 151838 Hom.: 14656 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.430 AC: 65413 AN: 151954 Hom.: 14657 Cov.: 32 AF XY: 0.429 AC XY: 31832 AN XY: 74264

African (AFR) AF: 0.309 AC: 12804 AN: 41430

American (AMR) AF: 0.429 AC: 6562 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1461 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1626 AN: 5164

South Asian (SAS) AF: 0.523 AC: 2518 AN: 4812

European-Finnish (FIN) AF: 0.409 AC: 4303 AN: 10528

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34668 AN: 67948

Other (OTH) AF: 0.422 AC: 889 AN: 2106

Alfa AF: 0.482 Hom.: 55002

Bravo AF: 0.423

Asia WGS AF: 0.444 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.89
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7086917; hg19: chr10-50197435;