rs716985

Variant names:

• chr4-18625889-T-G
• rs716985
• ENST00000652661.1:n.419-3211T>G

Variant summary

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

The ENST00000652661.1(ENSG00000286046):​n.419-3211T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,258 control chromosomes in the GnomAD database, including 239 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 0.041 (239 hom., cov: 33)
• Consequence: ENSG00000286046 ENST00000652661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 1 publications found

Genes affected

ENSG00000286046 (HGNC:59078):

LOC105374510 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652661.1. 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
	ENSG00000286046	ENST00000652661.1		n.419-3211T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6177 AN: 152140 Hom.: 235 Cov.: 33

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.0312

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00685

Gnomad OTH AF: 0.0379

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

GnomAD4 genome AF: 0.0407 AC: 6201 AN: 152258 Hom.: 239 Cov.: 33 AF XY: 0.0439 AC XY: 3265 AN XY: 74452

African (AFR) AF: 0.0694 AC: 2883 AN: 41542

American (AMR) AF: 0.0914 AC: 1398 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00202 AC: 7 AN: 3470

East Asian (EAS) AF: 0.122 AC: 635 AN: 5186

South Asian (SAS) AF: 0.0786 AC: 379 AN: 4824

European-Finnish (FIN) AF: 0.0312 AC: 331 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00685 AC: 466 AN: 68012

Other (OTH) AF: 0.0403 AC: 85 AN: 2108

Alfa AF: 0.0195 Hom.: 119

Bravo AF: 0.0450

Asia WGS AF: 0.121 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.44
PhyloP100		1.5

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: rs716985;

hg19: chr4-18627512;