2-41116081-G-C

Variant names:

• chr2-41116081-G-C
• rs2194437
• ENST00000753888.1:n.94+50382C>G

Variant summary

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

The ENST00000753888.1(ENSG00000298207):​n.94+50382C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 151,944 control chromosomes in the GnomAD database, including 4,077 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 0.16 (4077 hom., cov: 32)
• Consequence: ENSG00000298207 ENST00000753888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 2 publications found

Genes affected

ENSG00000298207 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753888.1. 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
	ENSG00000298207	ENST00000753888.1		n.94+50382C>G		intron	N/A
	ENSG00000298207	ENST00000753889.1		n.94+50382C>G		intron	N/A
	ENSG00000298207	ENST00000753890.1		n.190+10315C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24330 AN: 151826 Hom.: 4059 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.0929

Gnomad FIN AF: 0.0693

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0355

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.160 AC: 24383 AN: 151944 Hom.: 4077 Cov.: 32 AF XY: 0.159 AC XY: 11843 AN XY: 74260

African (AFR) AF: 0.414 AC: 17126 AN: 41382

American (AMR) AF: 0.112 AC: 1713 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1315 AN: 5162

South Asian (SAS) AF: 0.0921 AC: 443 AN: 4810

European-Finnish (FIN) AF: 0.0693 AC: 732 AN: 10562

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0355 AC: 2413 AN: 67982

Other (OTH) AF: 0.155 AC: 327 AN: 2106

Alfa AF: 0.0338 Hom.: 72

Bravo AF: 0.179

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.56
DANN	Benign	0.63
PhyloP100		-0.91

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: rs2194437;

hg19: chr2-41343221;