ENST00000813417.1:n.142-35205G>C

Variant names:

• chr6-113557780-C-G
• rs10499074
• ENST00000813417.1:n.142-35205G>C

Variant summary

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

The ENST00000813417.1(ENSG00000288916):​n.142-35205G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 152,248 control chromosomes in the GnomAD database, including 78 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 0.018 (78 hom., cov: 32)
• Consequence: ENSG00000288916 ENST00000813417.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 0 publications found

Genes affected

ENSG00000288916 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813417.1. 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
	ENSG00000288916	ENST00000813417.1		n.142-35205G>C		intron	N/A
	ENSG00000288916	ENST00000813418.1		n.167+29394G>C		intron	N/A
	ENSG00000288916	ENST00000813419.1		n.280+29394G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0183 AC: 2787 AN: 152130 Hom.: 78 Cov.: 32

Gnomad AFR AF: 0.00630

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.0538

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.00757

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0184 AC: 2797 AN: 152248 Hom.: 78 Cov.: 32 AF XY: 0.0203 AC XY: 1515 AN XY: 74456

African (AFR) AF: 0.00635 AC: 264 AN: 41546

American (AMR) AF: 0.0690 AC: 1055 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3468

East Asian (EAS) AF: 0.109 AC: 564 AN: 5186

South Asian (SAS) AF: 0.0537 AC: 259 AN: 4826

European-Finnish (FIN) AF: 0.00160 AC: 17 AN: 10598

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00757 AC: 515 AN: 68018

Other (OTH) AF: 0.0340 AC: 72 AN: 2116

Alfa AF: 0.00969 Hom.: 3

Bravo AF: 0.0230

Asia WGS AF: 0.0850 AC: 297 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.7
DANN	Benign	0.68
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs10499074; hg19: chr6-113878982;