rs17002253

chr4-76850192-T-C

Variant summary

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

The XM_047416557.1(LOC124900866):c.190-410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,224 control chromosomes in the GnomAD database, including 880 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 0.082 (880 hom., cov: 32)
• Consequence: LOC124900866 XM_047416557.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

LOC124900866 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900866	XM_047416557.1	c.190-410T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12409 AN: 152106 Hom.: 873 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0776

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0606

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0817 AC: 12433 AN: 152224 Hom.: 880 Cov.: 32 AF XY: 0.0820 AC XY: 6104 AN XY: 74440

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0780

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0606

Gnomad4 NFE AF: 0.0322

Gnomad4 OTH AF: 0.0630

Alfa AF: 0.0367 Hom.: 349

Bravo AF: 0.0840

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.3
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17002253; hg19: chr4-77771345;