rs7327522

chr13-20297156-G-A

Variant summary

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

The XR_941720.2(LOC105370102):n.106+1363G>A 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 0.659 in 151,592 control chromosomes in the GnomAD database, including 33,658 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 0.66 (33658 hom., cov: 30)
• Consequence: LOC105370102 XR_941720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

Genes affected

LOC105370102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370102	XR_941720.2	n.106+1363G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99752 AN: 151474 Hom.: 33637 Cov.: 30

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.659 AC: 99826 AN: 151592 Hom.: 33658 Cov.: 30 AF XY: 0.657 AC XY: 48642 AN XY: 74046

Gnomad4 AFR AF: 0.767

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.658

Alfa AF: 0.631 Hom.: 41827

Bravo AF: 0.672

Asia WGS AF: 0.531 AC: 1846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.4
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7327522; hg19: chr13-20871295;