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. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000236114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.529 AC: 37 AN: 70

American (AMR) AF: 0.786 AC: 22 AN: 28

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 4 AN: 8

East Asian (EAS) AF: 1.00 AC: 34 AN: 34

South Asian (SAS) AF: 0.677 AC: 65 AN: 96

European-Finnish (FIN) AF: 0.733 AC: 463 AN: 632

Middle Eastern (MID) AF: 0.667 AC: 873 AN: 1308

European-Non Finnish (NFE) AF: 0.672 AC: 316 AN: 470

Other (OTH) AF: 0.648 AC: 127 AN: 196

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

African (AFR) AF: 0.655 AC: 27164 AN: 41456

American (AMR) AF: 0.728 AC: 11117 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2010 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5155 AN: 5180

South Asian (SAS) AF: 0.747 AC: 3605 AN: 4824

European-Finnish (FIN) AF: 0.703 AC: 7412 AN: 10542

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.660 AC: 44859 AN: 67970

Other (OTH) AF: 0.696 AC: 1471 AN: 2114

Alfa AF: 0.665 Hom.: 11139

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3006365; hg19: chr10-44020675;