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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370302	XR_931625.3	n.486-14723A>G		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285699	ENST00000835138.1	n.604-14723A>G		intron_variant	Intron 5 of 8
ENSG00000285699	ENST00000835139.1	n.101-14723A>G		intron_variant	Intron 2 of 8
ENSG00000285699	ENST00000835140.1	n.80-14723A>G		intron_variant	Intron 1 of 2
ENSG00000285699	ENST00000835141.1	n.86-14723A>G		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs7321756; hg19: chr13-88061028;