rs10500368

Positions:

• chr16-9188654-G-A

Variant summary

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

The XR_007064980.1(LOC101927026):​n.72+3921G>A 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 0.0986 in 152,142 control chromosomes in the GnomAD database, including 1,608 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 0.099 (1608 hom., cov: 33)
• Consequence: LOC101927026 XR_007064980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200

Genes affected

LOC101927026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927026	XR_007064980.1	n.72+3921G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0983 AC: 14950 AN: 152024 Hom.: 1596 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0130

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0866

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

GnomAD4 genome AF: 0.0986 AC: 15007 AN: 152142 Hom.: 1608 Cov.: 33 AF XY: 0.0982 AC XY: 7306 AN XY: 74382

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.0838

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.0527

Gnomad4 FIN AF: 0.0130

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0857

Alfa AF: 0.0697 Hom.: 135

Bravo AF: 0.111

Asia WGS AF: 0.117 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10500368; hg19: chr16-9282511;