rs2327949

Variant names:

• chr6-16110214-G-A
• rs2327949
• ENST00000806821.1:n.590-11200G>A

Variant summary

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

The ENST00000806821.1(ENSG00000289953):​n.590-11200G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,152 control chromosomes in the GnomAD database, including 3,781 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 0.22 (3781 hom., cov: 32)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 2 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806821.1. 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
	ENSG00000289953	ENST00000806821.1		n.590-11200G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32798 AN: 152034 Hom.: 3774 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.216 AC: 32818 AN: 152152 Hom.: 3781 Cov.: 32 AF XY: 0.218 AC XY: 16184 AN XY: 74358

African (AFR) AF: 0.135 AC: 5610 AN: 41536

American (AMR) AF: 0.266 AC: 4066 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3464

East Asian (EAS) AF: 0.259 AC: 1339 AN: 5170

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4826

European-Finnish (FIN) AF: 0.264 AC: 2793 AN: 10560

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16439 AN: 67986

Other (OTH) AF: 0.184 AC: 389 AN: 2114

Alfa AF: 0.233 Hom.: 7404

Bravo AF: 0.213

Asia WGS AF: 0.241 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.4
DANN	Benign	0.86
PhyloP100		-0.0020

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: rs2327949;

hg19: chr6-16110445;