rs16078

Positions:

• chr7-24313836-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_001745132.2(LOC107986777):​n.209+5521C>T 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 0.03 in 152,244 control chromosomes in the GnomAD database, including 91 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 0.030 (91 hom., cov: 33)
• Consequence: LOC107986777 XR_001745132.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

LOC107986777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.03 (4560/152244) while in subpopulation NFE AF= 0.0419 (2848/68004). AF 95% confidence interval is 0.0406. There are 91 homozygotes in gnomad4. There are 2201 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 91 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986777	XR_001745132.2	n.209+5521C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0300 AC: 4562 AN: 152128 Hom.: 91 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.0224

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0300 AC: 4560 AN: 152244 Hom.: 91 Cov.: 33 AF XY: 0.0296 AC XY: 2201 AN XY: 74450

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.0411

Gnomad4 NFE AF: 0.0419

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0406 Hom.: 17

Bravo AF: 0.0271

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16078; hg19: chr7-24353455;