chr5-152354548-C-T

Variant names:

• chr5-152354548-C-T
• rs1010254
• XR_944433.2:n.197+16685C>T

Variant summary

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

The XR_944433.2(LOC105378237):​n.197+16685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,944 control chromosomes in the GnomAD database, including 9,603 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 0.34 (9603 hom., cov: 32)
• Consequence: LOC105378237 XR_944433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

Genes affected

LOC105378237 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378237	XR_944433.2	n.197+16685C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51585 AN: 151826 Hom.: 9581 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.340 AC: 51649 AN: 151944 Hom.: 9603 Cov.: 32 AF XY: 0.339 AC XY: 25150 AN XY: 74280

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.335

Alfa AF: 0.272 Hom.: 11509

Bravo AF: 0.354

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010254; hg19: chr5-151734109;