rs6517581

Variant names:

• chr21-39982941-G-A
• rs6517581
• ENST00000836969.1:n.383+1431C>T

Variant summary

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

The ENST00000836969.1(ENSG00000308873):​n.383+1431C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,082 control chromosomes in the GnomAD database, including 22,347 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 0.53 (22347 hom., cov: 33)
• Consequence: ENSG00000308873 ENST00000836969.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 1 publications found

Genes affected

ENSG00000308873 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836969.1. 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
	ENSG00000308873	ENST00000836969.1		n.383+1431C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81242 AN: 151962 Hom.: 22329 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.534 AC: 81281 AN: 152082 Hom.: 22347 Cov.: 33 AF XY: 0.527 AC XY: 39177 AN XY: 74326

African (AFR) AF: 0.530 AC: 21995 AN: 41486

American (AMR) AF: 0.437 AC: 6676 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2239 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1214 AN: 5170

South Asian (SAS) AF: 0.469 AC: 2260 AN: 4818

European-Finnish (FIN) AF: 0.524 AC: 5533 AN: 10558

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39665 AN: 67978

Other (OTH) AF: 0.563 AC: 1189 AN: 2112

Alfa AF: 0.562 Hom.: 109910

Bravo AF: 0.524

Asia WGS AF: 0.393 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.79
PhyloP100		-0.49

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: rs6517581;

hg19: chr21-41354868;