rs17550532

chr16-9650238-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.943-5213A>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 0.17 in 152,170 control chromosomes in the GnomAD database, including 2,433 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 0.17 (2433 hom., cov: 32)
• Consequence: LOC101927026 XR_007064980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

Genes affected

LOC101927026 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927026	XR_007064980.1	n.943-5213A>G		intron_variant, non_coding_transcript_variant
LOC101927026	XR_001752074.2	n.644-5213A>G		intron_variant, non_coding_transcript_variant
LOC101927026	XR_007064979.1	n.571-5213A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25929 AN: 152052 Hom.: 2435 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0780

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.170 AC: 25934 AN: 152170 Hom.: 2433 Cov.: 32 AF XY: 0.167 AC XY: 12390 AN XY: 74406

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0783

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.204

Alfa AF: 0.203 Hom.: 6839

Bravo AF: 0.167

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17550532; hg19: chr16-9744095;