5-4196382-G-C

Variant names:

• chr5-4196382-G-C
• rs10043296
• ENST00000762810.1:n.547-1687G>C

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.547-1687G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 152,274 control chromosomes in the GnomAD database, including 67,003 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 0.94 (67003 hom., cov: 33)
• Consequence: ENSG00000299354 ENST00000762810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 1 publications found

Genes affected

ENSG00000299354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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
ENSG00000299354	ENST00000762810.1	n.547-1687G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142642 AN: 152156 Hom.: 66968 Cov.: 33

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.958

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.937 AC: 142728 AN: 152274 Hom.: 67003 Cov.: 33 AF XY: 0.939 AC XY: 69878 AN XY: 74438

African (AFR) AF: 0.893 AC: 37111 AN: 41538

American (AMR) AF: 0.958 AC: 14659 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3318 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5137 AN: 5166

South Asian (SAS) AF: 0.905 AC: 4366 AN: 4822

European-Finnish (FIN) AF: 0.982 AC: 10423 AN: 10616

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.950 AC: 64602 AN: 68034

Other (OTH) AF: 0.928 AC: 1963 AN: 2116

Alfa AF: 0.947 Hom.: 8480

Bravo AF: 0.935

Asia WGS AF: 0.917 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.086
DANN	Benign	0.44
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10043296; hg19: chr5-4196495;