rs9980967

Variant names:

• chr21-45613991-C-A
• rs9980967
• ENST00000651182.1:n.382+1608G>T

Your query was ambiguous. Multiple possible variants found:

• chr21-45613991-C-A
• chr21-45613991-C-T

Variant summary

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

The ENST00000651182.1(ENSG00000286082):​n.382+1608G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 152,128 control chromosomes in the GnomAD database, including 759 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 0.095 (759 hom., cov: 31)
• Consequence: ENSG00000286082 ENST00000651182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 3 publications found

Genes affected

ENSG00000286082 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651182.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286082	ENST00000651182.1		n.382+1608G>T		intron	N/A
	ENSG00000286082	ENST00000820224.1		n.180+1608G>T		intron	N/A
	ENSG00000286082	ENST00000820225.1		n.281+1608G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14457 AN: 152010 Hom.: 758 Cov.: 31

Gnomad AFR AF: 0.0694

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0742

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0855

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.0951 AC: 14465 AN: 152128 Hom.: 759 Cov.: 31 AF XY: 0.0933 AC XY: 6939 AN XY: 74372

African (AFR) AF: 0.0695 AC: 2882 AN: 41496

American (AMR) AF: 0.0741 AC: 1134 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3468

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5174

South Asian (SAS) AF: 0.0630 AC: 304 AN: 4822

European-Finnish (FIN) AF: 0.0855 AC: 905 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8457 AN: 67968

Other (OTH) AF: 0.0948 AC: 200 AN: 2110

Alfa AF: 0.0989 Hom.: 476

Bravo AF: 0.0923

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9980967;

hg19: chr21-47033905;