rs9976523

Variant names:

• chr21-45612481-G-A
• rs9976523
• ENST00000820536.1:n.843G>A

Variant summary

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

The ENST00000820536.1(ENSG00000286594):​n.843G>A 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 0.0933 in 152,258 control chromosomes in the GnomAD database, including 739 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 0.093 (739 hom., cov: 31)
• Consequence: ENSG00000286594 ENST00000820536.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 0 publications found

Genes affected

ENSG00000286594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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: ENST00000820536.1. 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
	ENSG00000286594	ENST00000820536.1		n.843G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000286594	ENST00000820537.1		n.591G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000286082	ENST00000651182.1		n.382+3118C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14204 AN: 152140 Hom.: 738 Cov.: 31

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.0623

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0929

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

GnomAD4 genome AF: 0.0933 AC: 14212 AN: 152258 Hom.: 739 Cov.: 31 AF XY: 0.0911 AC XY: 6785 AN XY: 74448

African (AFR) AF: 0.0633 AC: 2628 AN: 41538

American (AMR) AF: 0.0740 AC: 1132 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.0214 AC: 111 AN: 5184

South Asian (SAS) AF: 0.0628 AC: 303 AN: 4828

European-Finnish (FIN) AF: 0.0858 AC: 910 AN: 10606

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8465 AN: 68016

Other (OTH) AF: 0.0919 AC: 194 AN: 2110

Alfa AF: 0.102 Hom.: 332

Bravo AF: 0.0905

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.57
PhyloP100		0.16

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: rs9976523;

hg19: chr21-47032395;