rs3006365

Variant names:

• chr10-43525227-C-A
• rs3006365
• ENST00000421913.1:n.*10C>A

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000421913.1(ENSG00000236114):​n.*10C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: ENSG00000236114 ENST00000421913.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

ENSG00000236114 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;