chr3-99345087-G-C

Variant names:

• chr3-99345087-G-C
• rs900060
• ENST00000715235.1:n.51+13635G>C

Variant summary

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

The ENST00000715235.1(ENSG00000243296):​n.51+13635G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 151,934 control chromosomes in the GnomAD database, including 2,398 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 0.16 (2398 hom., cov: 32)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 2 publications found

Genes affected

ENSG00000243296 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243296	ENST00000715235.1		n.51+13635G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23824 AN: 151816 Hom.: 2394 Cov.: 32

Gnomad AFR AF: 0.0575

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.0178

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.157 AC: 23836 AN: 151934 Hom.: 2398 Cov.: 32 AF XY: 0.154 AC XY: 11424 AN XY: 74244

African (AFR) AF: 0.0574 AC: 2379 AN: 41466

American (AMR) AF: 0.192 AC: 2929 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5168

South Asian (SAS) AF: 0.122 AC: 587 AN: 4804

European-Finnish (FIN) AF: 0.208 AC: 2189 AN: 10518

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14795 AN: 67944

Other (OTH) AF: 0.162 AC: 341 AN: 2108

Alfa AF: 0.0914 Hom.: 147

Bravo AF: 0.153

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs900060; hg19: chr3-99063931;