rs1880670

Variant names:

• chr1-109398511-C-T
• rs1880670
• ENST00000836084.1:n.332C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000836084.1(ENSG00000308734):​n.332C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,030 control chromosomes in the GnomAD database, including 33,699 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 0.65 (33699 hom., cov: 32)
• Consequence: ENSG00000308734 ENST00000836084.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 10 publications found

Genes affected

ENSG00000308734 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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
ENSG00000308734	ENST00000836084.1	n.332C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000308734	ENST00000836085.1	n.298C>T		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98336 AN: 151912 Hom.: 33680 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.647 AC: 98374 AN: 152030 Hom.: 33699 Cov.: 32 AF XY: 0.651 AC XY: 48408 AN XY: 74304

African (AFR) AF: 0.408 AC: 16927 AN: 41456

American (AMR) AF: 0.777 AC: 11881 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2863 AN: 3470

East Asian (EAS) AF: 0.958 AC: 4957 AN: 5174

South Asian (SAS) AF: 0.733 AC: 3529 AN: 4814

European-Finnish (FIN) AF: 0.709 AC: 7482 AN: 10556

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48438 AN: 67960

Other (OTH) AF: 0.700 AC: 1477 AN: 2110

Alfa AF: 0.648 Hom.: 4980

Bravo AF: 0.647

Asia WGS AF: 0.796 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.88
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1880670; hg19: chr1-109941133;