rs7086917

Positions:

• chr10-48989390-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422966.1(ENSG00000226576):​n.402+4425G>T variant causes a intron, non coding transcript 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: ENST00000422966.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422966.1	n.402+4425G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000428825.8	n.637+3020C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.422

Alfa AF: 0.495 Hom.: 36855

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7086917; hg19: chr10-50197435;