rs7332465

Positions:

• chr13-22095568-G-A
• chr13-22095568-G-C

Variant summary

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

The XR_007063716.1(LOC105370108):​n.22535G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,080 control chromosomes in the GnomAD database, including 34,701 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 0.65 (34701 hom., cov: 32)
• Consequence: LOC105370108 XR_007063716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

LOC105370108 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370108	XR_007063716.1	n.22535G>A		non_coding_transcript_exon_variant	4/4
LOC105370108	XR_007063715.1	n.24400G>A		non_coding_transcript_exon_variant	3/3
LOC105370108	XR_001749777.2	n.2668+21732G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000631321.1	n.410+54184G>A		intron_variant, non_coding_transcript_variant		2
LINC00540	ENST00000657205.1	n.413+54184G>A		intron_variant, non_coding_transcript_variant
LINC00540	ENST00000690279.1	n.411-17230G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98453 AN: 151962 Hom.: 34695 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.648 AC: 98481 AN: 152080 Hom.: 34701 Cov.: 32 AF XY: 0.647 AC XY: 48122 AN XY: 74362

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.675

Alfa AF: 0.758 Hom.: 55524

Bravo AF: 0.630

Asia WGS AF: 0.683 AC: 2375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7332465; hg19: chr13-22669707;