chr16-9287105-A-G

Position:

• chr16-9287105-A-G

Variant summary

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

The XR_007064980.1(LOC101927026):​n.72+102372A>G 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 0.624 in 151,910 control chromosomes in the GnomAD database, including 30,456 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 0.62 (30456 hom., cov: 31)
• Consequence: LOC101927026 XR_007064980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732

Genes affected

LOC101927026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927026	XR_007064980.1	n.72+102372A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94705 AN: 151792 Hom.: 30442 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.624 AC: 94749 AN: 151910 Hom.: 30456 Cov.: 31 AF XY: 0.625 AC XY: 46379 AN XY: 74230

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.674

Alfa AF: 0.656 Hom.: 16210

Bravo AF: 0.623

Asia WGS AF: 0.679 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1213205; hg19: chr16-9380962;