rs1420290

Variant names:

• chr16-54490313-G-A
• rs1420290
• ENST00000660981.1:n.1002C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-54490313-G-A
• chr16-54490313-G-C
• chr16-54490313-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000660981.1(ENSG00000286845):​n.1002C>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 0.884 in 152,258 control chromosomes in the GnomAD database, including 59,818 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 0.88 (59818 hom., cov: 34)
• Consequence: ENSG00000286845 ENST00000660981.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26

Genes affected

ENSG00000286845 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.915 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
ENSG00000286845	ENST00000660981.1	n.1002C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134451 AN: 152140 Hom.: 59765 Cov.: 34

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.884 AC: 134558 AN: 152258 Hom.: 59818 Cov.: 34 AF XY: 0.888 AC XY: 66106 AN XY: 74450

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.901

Alfa AF: 0.913 Hom.: 34391

Bravo AF: 0.876

Asia WGS AF: 0.889 AC: 3091 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	12
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1420290; hg19: chr16-54524225;