chr10-31291676-C-A

Position:

• chr10-31291676-C-A

Variant summary

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

The variant allele was found at a frequency of 0.138 in 151,830 control chromosomes in the GnomAD database, including 2,737 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 0.14 (2737 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.31291676C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZEB1-AS1	ENST00000605946.1	n.177+27839G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20957 AN: 151712 Hom.: 2720 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0663

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0471

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.138 AC: 21010 AN: 151830 Hom.: 2737 Cov.: 31 AF XY: 0.139 AC XY: 10328 AN XY: 74212

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.0662

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0853

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.0471

Gnomad4 OTH AF: 0.114

Alfa AF: 0.100 Hom.: 283

Bravo AF: 0.149

Asia WGS AF: 0.118 AC: 409 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	9.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16932309; hg19: chr10-31580605;