3-187838904-G-C

Variant names:

• chr3-187838904-G-C
• rs2611611
• ENST00000793661.1:n.344-5363C>G

Variant summary

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

The ENST00000793661.1(ENSG00000303324):​n.344-5363C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 149,318 control chromosomes in the GnomAD database, including 16,770 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 0.45 (16770 hom., cov: 28)
• Consequence: ENSG00000303324 ENST00000793661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962
• Publications: 3 publications found

Genes affected

ENSG00000303324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793661.1. 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
	ENSG00000303324	ENST00000793661.1		n.344-5363C>G		intron	N/A
	ENSG00000303324	ENST00000793662.1		n.601-22834C>G		intron	N/A
	ENSG00000303324	ENST00000793663.1		n.616+38103C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 66450 AN: 149200 Hom.: 16746 Cov.: 28

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.445 AC: 66513 AN: 149318 Hom.: 16770 Cov.: 28 AF XY: 0.440 AC XY: 31960 AN XY: 72618

African (AFR) AF: 0.698 AC: 28566 AN: 40902

American (AMR) AF: 0.313 AC: 4614 AN: 14764

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1067 AN: 3436

East Asian (EAS) AF: 0.287 AC: 1449 AN: 5040

South Asian (SAS) AF: 0.332 AC: 1517 AN: 4564

European-Finnish (FIN) AF: 0.375 AC: 3800 AN: 10124

Middle Eastern (MID) AF: 0.376 AC: 109 AN: 290

European-Non Finnish (NFE) AF: 0.361 AC: 24294 AN: 67236

Other (OTH) AF: 0.409 AC: 839 AN: 2052

Alfa AF: 0.284 Hom.: 725

Bravo AF: 0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.32
PhyloP100		-0.96

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: rs2611611;

hg19: chr3-187556692;