rs10492775

Positions:

• chr16-13527425-T-C

Variant summary

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

The ENST00000655174.1(ENSG00000262801):​n.534-35282T>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 0.0822 in 152,192 control chromosomes in the GnomAD database, including 574 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 0.082 (574 hom., cov: 32)
• Consequence: ENST00000655174.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHISA9	XR_007064905.1	n.1689-24968T>C		intron_variant, non_coding_transcript_variant
SHISA9	XR_932915.3	n.1689-35282T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655174.1	n.534-35282T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12498 AN: 152074 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0933

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.0975

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

GnomAD4 genome AF: 0.0822 AC: 12509 AN: 152192 Hom.: 574 Cov.: 32 AF XY: 0.0838 AC XY: 6237 AN XY: 74398

Gnomad4 AFR AF: 0.0549

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.0517

Gnomad4 NFE AF: 0.0795

Gnomad4 OTH AF: 0.0960

Alfa AF: 0.0817 Hom.: 63

Bravo AF: 0.0901

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492775; hg19: chr16-13621282;