5-176899947-C-G

Variant names:

• chr5-176899947-C-G
• rs3762971
• ENST00000754646.1:n.217+286C>G

Variant summary

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

The ENST00000754646.1(ENSG00000298307):​n.217+286C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,230 control chromosomes in the GnomAD database, including 61,297 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 0.90 (61297 hom., cov: 31)
• Consequence: ENSG00000298307 ENST00000754646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 7 publications found

Genes affected

ENSG00000298307 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298307	ENST00000754646.1	n.217+286C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136352 AN: 152112 Hom.: 61235 Cov.: 31

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.896 AC: 136473 AN: 152230 Hom.: 61297 Cov.: 31 AF XY: 0.897 AC XY: 66764 AN XY: 74424

African (AFR) AF: 0.947 AC: 39364 AN: 41552

American (AMR) AF: 0.911 AC: 13934 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3036 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5110 AN: 5172

South Asian (SAS) AF: 0.916 AC: 4413 AN: 4818

European-Finnish (FIN) AF: 0.861 AC: 9123 AN: 10592

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58580 AN: 68006

Other (OTH) AF: 0.886 AC: 1870 AN: 2110

Alfa AF: 0.870 Hom.: 2783

Bravo AF: 0.902

Asia WGS AF: 0.939 AC: 3261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.49
PhyloP100		0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3762971; hg19: chr5-176326948;