rs3100717

Variant names:

• chr2-138016981-C-T
• rs3100717
• ENST00000838313.1:n.229-9185G>A

Variant summary

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

The ENST00000838313.1(ENSG00000309081):​n.229-9185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,952 control chromosomes in the GnomAD database, including 9,020 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 0.31 (9020 hom., cov: 32)
• Consequence: ENSG00000309081 ENST00000838313.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 6 publications found

Genes affected

ENSG00000309081 (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 (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838313.1. 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
	ENSG00000309081	ENST00000838313.1		n.229-9185G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47756 AN: 151832 Hom.: 8996 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.315 AC: 47848 AN: 151952 Hom.: 9020 Cov.: 32 AF XY: 0.318 AC XY: 23585 AN XY: 74268

African (AFR) AF: 0.521 AC: 21590 AN: 41444

American (AMR) AF: 0.330 AC: 5038 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1407 AN: 5160

South Asian (SAS) AF: 0.305 AC: 1468 AN: 4810

European-Finnish (FIN) AF: 0.255 AC: 2697 AN: 10556

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13675 AN: 67954

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.277 Hom.: 1123

Bravo AF: 0.329

Asia WGS AF: 0.352 AC: 1221 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	4.9
DANN	Benign	0.24
PhyloP100		1.2

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: rs3100717;

hg19: chr2-138774551;