chr5-107782439-G-T

Variant names:

• chr5-107782439-G-T
• rs770182
• ENST00000737254.1:n.474+1476G>T

Variant summary

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

The ENST00000737254.1(ENSG00000296200):​n.474+1476G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,954 control chromosomes in the GnomAD database, including 33,797 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 0.67 (33797 hom., cov: 31)
• Consequence: ENSG00000296200 ENST00000737254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 5 publications found

Genes affected

ENSG00000296200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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
ENSG00000296200	ENST00000737254.1	n.474+1476G>T		intron_variant	Intron 2 of 2
ENSG00000296200	ENST00000737255.1	n.258-7570G>T		intron_variant	Intron 1 of 1
ENSG00000296200	ENST00000737256.1	n.401+1507G>T		intron_variant	Intron 2 of 2
ENSG00000296200	ENST00000737257.1	n.431+1472G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101088 AN: 151834 Hom.: 33751 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.666 AC: 101186 AN: 151954 Hom.: 33797 Cov.: 31 AF XY: 0.662 AC XY: 49181 AN XY: 74268

African (AFR) AF: 0.614 AC: 25456 AN: 41448

American (AMR) AF: 0.718 AC: 10935 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2423 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4174 AN: 5170

South Asian (SAS) AF: 0.642 AC: 3098 AN: 4824

European-Finnish (FIN) AF: 0.584 AC: 6163 AN: 10546

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46857 AN: 67962

Other (OTH) AF: 0.679 AC: 1431 AN: 2106

Alfa AF: 0.687 Hom.: 111381

Bravo AF: 0.676

Asia WGS AF: 0.742 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.82
DANN	Benign	0.68
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs770182; hg19: chr5-107118140; COSMIC: COSV69025974;