rs349114

chr13-97551473-G-A

Variant summary

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

The XR_007063845.1(LOC105370324):n.2615-4122C>T 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 0.165 in 152,058 control chromosomes in the GnomAD database, including 2,396 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 0.16 (2396 hom., cov: 32)
• Consequence: LOC105370324 XR_007063845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

Genes affected

LOC105370324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370324	XR_007063845.1	n.2615-4122C>T		intron_variant, non_coding_transcript_variant
LOC105370324	XR_931663.3	n.2671-4122C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25038 AN: 151940 Hom.: 2391 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.165 AC: 25051 AN: 152058 Hom.: 2396 Cov.: 32 AF XY: 0.163 AC XY: 12123 AN XY: 74318

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0979

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.140

Alfa AF: 0.184 Hom.: 2747

Bravo AF: 0.160

Asia WGS AF: 0.179 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.80
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs349114; hg19: chr13-98203727;