rs2016167

Variant names:

• chr5-113714894-G-T
• rs2016167
• ENST00000810863.1:n.794+237G>T

Variant summary

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

The ENST00000810863.1(ENSG00000305424):​n.794+237G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,178 control chromosomes in the GnomAD database, including 3,663 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 0.20 (3663 hom., cov: 33)
• Consequence: ENSG00000305424 ENST00000810863.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 1 publications found

Genes affected

ENSG00000305424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810863.1. 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
	ENSG00000305424	ENST00000810863.1		n.794+237G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30934 AN: 152060 Hom.: 3662 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.203 AC: 30964 AN: 152178 Hom.: 3663 Cov.: 33 AF XY: 0.197 AC XY: 14653 AN XY: 74410

African (AFR) AF: 0.329 AC: 13670 AN: 41492

American (AMR) AF: 0.171 AC: 2620 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 411 AN: 3472

East Asian (EAS) AF: 0.0231 AC: 120 AN: 5188

South Asian (SAS) AF: 0.0930 AC: 449 AN: 4826

European-Finnish (FIN) AF: 0.148 AC: 1569 AN: 10590

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11596 AN: 68006

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.200 Hom.: 428

Bravo AF: 0.209

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.17
PhyloP100		-2.5

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: rs2016167;

hg19: chr5-113050591;