16-54490313-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000286845 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660981.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286845	ENST00000660981.1		n.1002C>T		non_coding_transcript_exon	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

African (AFR) AF: 0.778 AC: 32285 AN: 41518

American (AMR) AF: 0.926 AC: 14162 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3166 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4617 AN: 5174

South Asian (SAS) AF: 0.909 AC: 4385 AN: 4824

European-Finnish (FIN) AF: 0.969 AC: 10293 AN: 10622

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.921 AC: 62634 AN: 68032

Other (OTH) AF: 0.901 AC: 1905 AN: 2114

Alfa AF: 0.909 Hom.: 47953

Bravo AF: 0.876

Asia WGS AF: 0.889 AC: 3091 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1420290; hg19: chr16-54524225;