chr1-84295665-T-C

Variant names:

• chr1-84295665-T-C
• rs1085093
• ENST00000721912.1:n.362A>G

Variant summary

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

The ENST00000721912.1(ENSG00000294213):​n.362A>G 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 0.787 in 152,148 control chromosomes in the GnomAD database, including 47,684 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 0.79 (47684 hom., cov: 32)
• Consequence: ENSG00000294213 ENST00000721912.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 11 publications found

Genes affected

ENSG00000294213 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
ENSG00000294213	ENST00000721912.1	n.362A>G		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000294213	ENST00000721911.1	n.744+1756A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119643 AN: 152030 Hom.: 47662 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.787 AC: 119709 AN: 152148 Hom.: 47684 Cov.: 32 AF XY: 0.788 AC XY: 58648 AN XY: 74400

African (AFR) AF: 0.662 AC: 27449 AN: 41466

American (AMR) AF: 0.792 AC: 12118 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3063 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5178 AN: 5184

South Asian (SAS) AF: 0.871 AC: 4193 AN: 4816

European-Finnish (FIN) AF: 0.814 AC: 8616 AN: 10590

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56390 AN: 68004

Other (OTH) AF: 0.791 AC: 1671 AN: 2112

Alfa AF: 0.832 Hom.: 40697

Bravo AF: 0.779

Asia WGS AF: 0.911 AC: 3165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1085093; hg19: chr1-84761348;