rs1420290

chr16-54490313-G-Achr16-54490313-G-Cchr16-54490313-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: ENST00000660981.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660981.1	n.1002C>T		non_coding_transcript_exon_variant	2/2

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;