rs7047636

Positions:

• chr9-99817185-C-G
• chr9-99817185-C-T

Variant summary

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

The NR_109802.1(LOC101928438):​n.69+2636G>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 0.359 in 151,942 control chromosomes in the GnomAD database, including 10,116 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 0.36 (10116 hom., cov: 32)
• Consequence: LOC101928438 NR_109802.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

Genes affected

(HGNC:):

STX17-DT (HGNC:51174): (STX17 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928438	NR_109802.1	n.69+2636G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652827.1	n.101+2636G>C		intron_variant, non_coding_transcript_variant
STX17-DT	ENST00000655615.1	n.268+21801G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54485 AN: 151824 Hom.: 10097 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.359 AC: 54547 AN: 151942 Hom.: 10116 Cov.: 32 AF XY: 0.350 AC XY: 26024 AN XY: 74268

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.370

Alfa AF: 0.363 Hom.: 1214

Bravo AF: 0.362

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7047636; hg19: chr9-102579467;