rs8048671

chr16-13242587-C-G

Variant summary

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

The XM_047434582.1(SHISA9):c.970+39038C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,156 control chromosomes in the GnomAD database, including 5,112 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 0.25 (5112 hom., cov: 32)
• Consequence: SHISA9 XM_047434582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

SHISA9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHISA9	XM_011522642.3	c.970+39038C>G		intron_variant
SHISA9	XM_047434582.1	c.970+39038C>G		intron_variant
SHISA9	XR_007064905.1	n.1314+39038C>G		intron_variant, non_coding_transcript_variant
SHISA9	XR_932915.3	n.1314+39038C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38518 AN: 152038 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.253 AC: 38558 AN: 152156 Hom.: 5112 Cov.: 32 AF XY: 0.251 AC XY: 18637 AN XY: 74384

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.271

Alfa AF: 0.237 Hom.: 566

Bravo AF: 0.260

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.43
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8048671; hg19: chr16-13336444;