rs16960843

Positions:

• chr15-48374628-A-G
• chr15-48374628-A-T

Variant summary

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

The XR_007064623.1(LOC107984755):​n.544+24364T>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 0.0602 in 150,294 control chromosomes in the GnomAD database, including 763 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 0.060 (763 hom., cov: 32)
• Consequence: LOC107984755 XR_007064623.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

Genes affected

LOC107984755 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984755	XR_007064623.1	n.544+24364T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9018 AN: 150180 Hom.: 758 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.00696

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.00746

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0602 AC: 9053 AN: 150294 Hom.: 763 Cov.: 32 AF XY: 0.0641 AC XY: 4700 AN XY: 73334

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.00696

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.0633

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.00746

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0366 Hom.: 48

Bravo AF: 0.0742

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960843; hg19: chr15-48666825;