rs7992158

chr13-112435894-G-Achr13-112435894-G-Cchr13-112435894-G-T

Variant summary

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

The XR_944294.2(LOC105370372):n.329+39240C>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 0.558 in 152,122 control chromosomes in the GnomAD database, including 24,144 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 0.56 (24144 hom., cov: 33)
• Consequence: LOC105370372 XR_944294.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LOC105370372 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370372	XR_944294.2	n.329+39240C>T		intron_variant, non_coding_transcript_variant
LOC105370372	XR_001750036.1	n.384+39240C>T		intron_variant, non_coding_transcript_variant
LOC105370372	XR_944292.2	n.332+39240C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84785 AN: 152004 Hom.: 24138 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.558 AC: 84827 AN: 152122 Hom.: 24144 Cov.: 33 AF XY: 0.562 AC XY: 41822 AN XY: 74362

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.565

Alfa AF: 0.535 Hom.: 22544

Bravo AF: 0.560

Asia WGS AF: 0.702 AC: 2438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.31
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7992158; hg19: chr13-113090208;