chr13-96916842-C-G

Variant names:

• chr13-96916842-C-G
• rs7492028
• ENST00000838825.1:n.191-16601C>G

Variant summary

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

The ENST00000838825.1(ENSG00000309124):​n.191-16601C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,072 control chromosomes in the GnomAD database, including 11,014 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 0.26 (11014 hom., cov: 32)
• Consequence: ENSG00000309124 ENST00000838825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 3 publications found

Genes affected

ENSG00000309124 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000838825.1. 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
	ENSG00000309124	ENST00000838825.1		n.191-16601C>G		intron	N/A
	ENSG00000309124	ENST00000838826.1		n.260-1560C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39536 AN: 151954 Hom.: 10981 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0433

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.261 AC: 39627 AN: 152072 Hom.: 11014 Cov.: 32 AF XY: 0.252 AC XY: 18743 AN XY: 74340

African (AFR) AF: 0.704 AC: 29202 AN: 41474

American (AMR) AF: 0.145 AC: 2218 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0874 AC: 303 AN: 3466

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5172

South Asian (SAS) AF: 0.0673 AC: 324 AN: 4814

European-Finnish (FIN) AF: 0.0433 AC: 458 AN: 10580

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0939 AC: 6385 AN: 67988

Other (OTH) AF: 0.224 AC: 473 AN: 2108

Alfa AF: 0.0277 Hom.: 25

Bravo AF: 0.287

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.18
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs7492028; hg19: chr13-97569096;