rs35455143

Positions:

• chr12-102556815-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0361 in 152,158 control chromosomes in the GnomAD database, including 139 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 0.036 (139 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0361 (5486/152158) while in subpopulation NFE AF= 0.0447 (3039/67990). AF 95% confidence interval is 0.0434. There are 139 homozygotes in gnomad4. There are 2714 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 139 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.102556815C>T		intergenic_region
LINC02456	XR_007063427.1	n.34902+72927C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5482 AN: 152040 Hom.: 139 Cov.: 32

Gnomad AFR AF: 0.0239

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0868

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0361 AC: 5486 AN: 152158 Hom.: 139 Cov.: 32 AF XY: 0.0365 AC XY: 2714 AN XY: 74408

Gnomad4 AFR AF: 0.0239

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00706

Gnomad4 FIN AF: 0.0868

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0398 Hom.: 19

Bravo AF: 0.0305

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	12
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35455143; hg19: chr12-102950593;