rs2716900

Variant names:

• chr17-5706770-C-A
• rs2716900
• ENST00000783338.1:n.187-6225G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-5706770-C-A
• chr17-5706770-C-T

Variant summary

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

The ENST00000783338.1(ENSG00000286356):​n.187-6225G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,034 control chromosomes in the GnomAD database, including 5,750 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 0.25 (5750 hom., cov: 32)
• Consequence: ENSG00000286356 ENST00000783338.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 2 publications found

Genes affected

ENSG00000286356 (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 = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000783338.1. 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
	ENSG00000286356	ENST00000783338.1		n.187-6225G>T		intron	N/A
	ENSG00000286356	ENST00000783339.1		n.240-6225G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38571 AN: 151916 Hom.: 5746 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.254 AC: 38594 AN: 152034 Hom.: 5750 Cov.: 32 AF XY: 0.251 AC XY: 18648 AN XY: 74280

African (AFR) AF: 0.137 AC: 5692 AN: 41508

American (AMR) AF: 0.195 AC: 2979 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 883 AN: 3468

East Asian (EAS) AF: 0.101 AC: 520 AN: 5160

South Asian (SAS) AF: 0.112 AC: 538 AN: 4810

European-Finnish (FIN) AF: 0.383 AC: 4035 AN: 10532

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23189 AN: 67962

Other (OTH) AF: 0.249 AC: 524 AN: 2106

Alfa AF: 0.243 Hom.: 1157

Bravo AF: 0.236

Asia WGS AF: 0.100 AC: 352 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	0.032
DANN	Benign	0.83
PhyloP100		-2.1

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: rs2716900;

hg19: chr17-5610090;