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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374264	XR_924813.3	n.606-2725C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303324	ENST00000793661.1	n.344-5363C>G		intron_variant	Intron 2 of 6
ENSG00000303324	ENST00000793662.1	n.601-22834C>G		intron_variant	Intron 2 of 4
ENSG00000303324	ENST00000793663.1	n.616+38103C>G		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs2611611; hg19: chr3-187556692;