rs606490

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-10318343-G-A
• chr5-10318343-G-C
• chr5-10318343-G-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785097.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302231	ENST00000785097.1		n.306-737G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs606490;

hg19: chr5-10318455;