rs791888

chr10-87652818-G-T

Variant summary

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

The ENST00000354527.2(ENSG00000196566):n.146+7040C>A 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 0.356 in 151,904 control chromosomes in the GnomAD database, including 10,162 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 0.36 (10162 hom., cov: 32)
• Consequence: ENST00000354527.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000354527.2	n.146+7040C>A		intron_variant, non_coding_transcript_variant		3
	ENST00000438082.1	n.109-5685G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54106 AN: 151786 Hom.: 10157 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.356 AC: 54151 AN: 151904 Hom.: 10162 Cov.: 32 AF XY: 0.347 AC XY: 25734 AN XY: 74242

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.369

Alfa AF: 0.417 Hom.: 17959

Bravo AF: 0.361

Asia WGS AF: 0.221 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.6
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs791888; hg19: chr10-89412575;