ENST00000785097.1:n.306-737G>A

Variant names:

• chr5-10318343-G-A
• rs606490
• ENST00000785097.1:n.306-737G>A

Variant summary

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

The ENST00000785097.1(ENSG00000302231):​n.306-737G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,144 control chromosomes in the GnomAD database, including 3,366 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 0.20 (3366 hom., cov: 31)
• Consequence: ENSG00000302231 ENST00000785097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 3 publications found

Genes affected

ENSG00000302231 (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 (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374651	XR_925783.3	n.42-737G>A		intron_variant	Intron 1 of 3
LOC105374651	XR_925786.3	n.42-737G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302231	ENST00000785097.1	n.306-737G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29947 AN: 152028 Hom.: 3363 Cov.: 31

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.197 AC: 29966 AN: 152144 Hom.: 3366 Cov.: 31 AF XY: 0.190 AC XY: 14163 AN XY: 74382

African (AFR) AF: 0.306 AC: 12682 AN: 41478

American (AMR) AF: 0.130 AC: 1981 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.0137 AC: 71 AN: 5188

South Asian (SAS) AF: 0.101 AC: 488 AN: 4826

European-Finnish (FIN) AF: 0.155 AC: 1644 AN: 10576

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12015 AN: 68008

Other (OTH) AF: 0.201 AC: 424 AN: 2114

Alfa AF: 0.179 Hom.: 10703

Bravo AF: 0.200

Asia WGS AF: 0.0710 AC: 248 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	1.5
DANN	Benign	0.37
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs606490; hg19: chr5-10318455;