rs13358260

Positions:

• chr5-79549888-T-C

Variant summary

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

The XR_948497.3(LOC105379047):​n.72+2244T>C 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 0.0622 in 152,198 control chromosomes in the GnomAD database, including 421 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 0.062 (421 hom., cov: 32)
• Consequence: LOC105379047 XR_948497.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.795

Genes affected

LOC105379047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379047	XR_948497.3	n.72+2244T>C		intron_variant, non_coding_transcript_variant
LOC105379047	XR_948498.3	n.159+2051T>C		intron_variant, non_coding_transcript_variant
LOC105379047	XR_948499.3	n.167+1586T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9451 AN: 152078 Hom.: 415 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.0981

Gnomad SAS AF: 0.0705

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0622 AC: 9464 AN: 152198 Hom.: 421 Cov.: 32 AF XY: 0.0642 AC XY: 4777 AN XY: 74402

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0902

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.0979

Gnomad4 SAS AF: 0.0705

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.0583

Alfa AF: 0.0693 Hom.: 491

Bravo AF: 0.0588

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13358260; hg19: chr5-78845711; COSMIC: COSV50461287;