13-23083379-G-A

Variant names:

• chr13-23083379-G-A
• rs7335200
• ENST00000743290.1:n.229-783C>T

Variant summary

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

The ENST00000743290.1(ENSG00000296879):​n.229-783C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,102 control chromosomes in the GnomAD database, including 1,442 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 0.14 (1442 hom., cov: 32)
• Consequence: ENSG00000296879 ENST00000743290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 5 publications found

Genes affected

ENSG00000296879 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743290.1. 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
	ENSG00000296879	ENST00000743290.1		n.229-783C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20540 AN: 151984 Hom.: 1432 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.135 AC: 20573 AN: 152102 Hom.: 1442 Cov.: 32 AF XY: 0.139 AC XY: 10319 AN XY: 74362

African (AFR) AF: 0.161 AC: 6688 AN: 41494

American (AMR) AF: 0.117 AC: 1782 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 564 AN: 3470

East Asian (EAS) AF: 0.0896 AC: 464 AN: 5178

South Asian (SAS) AF: 0.139 AC: 670 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2019 AN: 10548

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7898 AN: 68000

Other (OTH) AF: 0.132 AC: 279 AN: 2110

Alfa AF: 0.121 Hom.: 1931

Bravo AF: 0.132

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.70
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs7335200; hg19: chr13-23657518;