10-87655391-G-A

Position:

• chr10-87655391-G-A

Variant summary

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

The ENST00000354527.2(ENSG00000196566):​n.146+4467C>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 0.663 in 151,878 control chromosomes in the GnomAD database, including 34,079 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 0.66 (34079 hom., cov: 31)
• Consequence: ENST00000354527.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.853

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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+4467C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000438082.1	n.109-3112G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100538 AN: 151760 Hom.: 34020 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.663 AC: 100655 AN: 151878 Hom.: 34079 Cov.: 31 AF XY: 0.658 AC XY: 48825 AN XY: 74208

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.649

Alfa AF: 0.624 Hom.: 3802

Bravo AF: 0.679

Asia WGS AF: 0.605 AC: 2106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1969821; hg19: chr10-89415148;