rs167021

Positions:

• chr13-67855812-C-T

Variant summary

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

The XR_942050.2(LOC105370251):​n.183+2160G>A 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 0.173 in 152,084 control chromosomes in the GnomAD database, including 2,439 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 0.17 (2439 hom., cov: 32)
• Consequence: LOC105370251 XR_942050.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.23

Genes affected

LOC105370251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370251	XR_942050.2	n.183+2160G>A		intron_variant, non_coding_transcript_variant
LOC105370251	XR_942049.3	n.183+2160G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26321 AN: 151968 Hom.: 2425 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.173 AC: 26367 AN: 152084 Hom.: 2439 Cov.: 32 AF XY: 0.172 AC XY: 12771 AN XY: 74352

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.208

Alfa AF: 0.204 Hom.: 6851

Bravo AF: 0.173

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	20
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs167021; hg19: chr13-68429944;