rs934073

Variant names:

• chr2-25714296-C-G
• rs934073
• ENST00000837714.1:n.217+7727G>C

Variant summary

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

The ENST00000837714.1(ENSG00000308999):​n.217+7727G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,970 control chromosomes in the GnomAD database, including 7,840 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 (7840 hom., cov: 32)
• Consequence: ENSG00000308999 ENST00000837714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 7 publications found

Genes affected

ENSG00000308999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837714.1. 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
	ENSG00000308999	ENST00000837714.1		n.217+7727G>C		intron	N/A
	ENSG00000308999	ENST00000837715.1		n.393-4924G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46714 AN: 151852 Hom.: 7807 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.0781

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.308 AC: 46811 AN: 151970 Hom.: 7840 Cov.: 32 AF XY: 0.301 AC XY: 22363 AN XY: 74260

African (AFR) AF: 0.419 AC: 17346 AN: 41402

American (AMR) AF: 0.244 AC: 3728 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3472

East Asian (EAS) AF: 0.0781 AC: 405 AN: 5184

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4814

European-Finnish (FIN) AF: 0.192 AC: 2024 AN: 10540

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20095 AN: 67990

Other (OTH) AF: 0.290 AC: 612 AN: 2112

Alfa AF: 0.319 Hom.: 1009

Bravo AF: 0.315

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.72
DANN	Benign	0.38
PhyloP100		-0.10

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: rs934073;

hg19: chr2-25937165;