rs7321756

Variant names:

• chr13-87408773-A-G
• rs7321756
• ENST00000835138.1:n.604-14723A>G

Variant summary

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

The ENST00000835138.1(ENSG00000285699):​n.604-14723A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,712 control chromosomes in the GnomAD database, including 1,993 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 0.15 (1993 hom., cov: 32)
• Consequence: ENSG00000285699 ENST00000835138.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 1 publications found

Genes affected

ENSG00000285699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835138.1. 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
	ENSG00000285699	ENST00000835138.1		n.604-14723A>G		intron	N/A
	ENSG00000285699	ENST00000835139.1		n.101-14723A>G		intron	N/A
	ENSG00000285699	ENST00000835140.1		n.80-14723A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22783 AN: 151596 Hom.: 1993 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.150 AC: 22791 AN: 151712 Hom.: 1993 Cov.: 32 AF XY: 0.146 AC XY: 10847 AN XY: 74152

African (AFR) AF: 0.234 AC: 9688 AN: 41432

American (AMR) AF: 0.116 AC: 1774 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 806 AN: 3470

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5172

South Asian (SAS) AF: 0.107 AC: 514 AN: 4822

European-Finnish (FIN) AF: 0.0937 AC: 981 AN: 10472

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8451 AN: 67792

Other (OTH) AF: 0.171 AC: 360 AN: 2106

Alfa AF: 0.138 Hom.: 355

Bravo AF: 0.154

Asia WGS AF: 0.0730 AC: 248 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.74
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7321756;

hg19: chr13-88061028;