13-20322479-T-C

Position:

• chr13-20322479-T-C

Variant summary

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

The XR_941720.2(LOC105370102):​n.200+1644T>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 0.401 in 152,146 control chromosomes in the GnomAD database, including 13,798 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 0.40 (13798 hom., cov: 32)
• Consequence: LOC105370102 XR_941720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

LOC105370102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370102	XR_941720.2	n.200+1644T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.401 AC: 61025 AN: 152028 Hom.: 13788 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.401 AC: 61075 AN: 152146 Hom.: 13798 Cov.: 32 AF XY: 0.399 AC XY: 29675 AN XY: 74372

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.413

Alfa AF: 0.486 Hom.: 33283

Bravo AF: 0.386

Asia WGS AF: 0.408 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.052
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7337231; hg19: chr13-20896618;