rs7321756

Positions:

• chr13-87408773-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931625.3(LOC105370302):​n.486-14723A>G variant causes a intron, non coding transcript 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: LOC105370302 XR_931625.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248

Genes affected

LOC105370302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105370302	XR_931625.3	n.486-14723A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.171

Alfa AF: 0.137 Hom.: 340

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7321756; hg19: chr13-88061028;