rs1075394

Positions:

• chr8-100392722-A-G

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 0.556 in 152,034 control chromosomes in the GnomAD database, including 23,728 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 0.56 (23728 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.100392722A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253824	ENST00000519844.2	n.153-10951T>C		intron_variant		3
ENSG00000253824	ENST00000523870.1	n.194+2659T>C		intron_variant		2
ENSG00000253824	ENST00000654832.1	n.181-10951T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84420 AN: 151916 Hom.: 23688 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.556 AC: 84520 AN: 152034 Hom.: 23728 Cov.: 32 AF XY: 0.553 AC XY: 41059 AN XY: 74314

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.557

Alfa AF: 0.532 Hom.: 35865

Bravo AF: 0.559

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075394; hg19: chr8-101404950;