4-10186702-G-A

Position:

• chr4-10186702-G-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 0.601 in 152,034 control chromosomes in the GnomAD database, including 28,330 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 0.60 (28330 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10186702G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91243 AN: 151916 Hom.: 28309 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.601 AC: 91301 AN: 152034 Hom.: 28330 Cov.: 32 AF XY: 0.602 AC XY: 44727 AN XY: 74296

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.596

Alfa AF: 0.664 Hom.: 67277

Bravo AF: 0.582

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs956312; hg19: chr4-10188326;