rs3006365

Positions:

• chr10-43525227-C-A
• chr10-43525227-C-G
• chr10-43525227-C-T

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 0.682 in 154,870 control chromosomes in the GnomAD database, including 36,358 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 0.68 (35676 hom., cov: 32)
  • Exomes 𝑓: 0.68 (682 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43525227C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000236114	ENST00000421913.1	n.*10C>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103535 AN: 151912 Hom.: 35644 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.693

GnomAD4 exome AF: 0.683 AC: 1941 AN: 2842 Hom.: 682 Cov.: 0 AF XY: 0.681 AC XY: 989 AN XY: 1452

Gnomad4 AFR exome AF: 0.529

Gnomad4 AMR exome AF: 0.786

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.677

Gnomad4 FIN exome AF: 0.733

Gnomad4 NFE exome AF: 0.672

Gnomad4 OTH exome AF: 0.648

GnomAD4 genome AF: 0.682 AC: 103614 AN: 152028 Hom.: 35676 Cov.: 32 AF XY: 0.688 AC XY: 51108 AN XY: 74304

Gnomad4 AFR AF: 0.655

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.747

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.696

Alfa AF: 0.623 Hom.: 4825

Bravo AF: 0.686

Asia WGS AF: 0.861 AC: 2991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.7
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3006365; hg19: chr10-44020675;