rs10507414

Variant names:

• chr13-33723706-C-G
• rs10507414
• ENST00000731018.1:n.194+23311C>G

Variant summary

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

The ENST00000731018.1(ENSG00000295576):​n.194+23311C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 152,214 control chromosomes in the GnomAD database, including 994 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 0.077 (994 hom., cov: 33)
• Consequence: ENSG00000295576 ENST00000731018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 3 publications found

Genes affected

ENSG00000295576 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731018.1. 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
	ENSG00000295576	ENST00000731018.1		n.194+23311C>G		intron	N/A
	ENSG00000288767	ENST00000731141.1		n.51-38127C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11725 AN: 152096 Hom.: 990 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0728

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0111

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0773 AC: 11763 AN: 152214 Hom.: 994 Cov.: 33 AF XY: 0.0786 AC XY: 5846 AN XY: 74414

African (AFR) AF: 0.191 AC: 7929 AN: 41492

American (AMR) AF: 0.0731 AC: 1118 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1297 AN: 5182

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4826

European-Finnish (FIN) AF: 0.0230 AC: 244 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0111 AC: 752 AN: 68026

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0456 Hom.: 66

Bravo AF: 0.0881

Asia WGS AF: 0.175 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs10507414; hg19: chr13-34297843;