19-49975675-T-C

Position:

• chr19-49975675-T-C

Variant summary

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

The NR_145574.2(SIGLEC16):​n.3668T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,178 control chromosomes in the GnomAD database, including 2,681 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 0.18 (2681 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SIGLEC16 NR_145574.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

SIGLEC16 (HGNC:24851): (sialic acid binding Ig like lectin 16) Predicted to enable sialic acid binding activity. Involved in positive regulation of defense response to bacterium and positive regulation of interleukin-6 production. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIGLEC16	NR_145574.2	n.3668T>C		non_coding_transcript_exon_variant	9/9
SIGLEC16	NM_001348364.2	c.*2188T>C		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIGLEC16	ENST00000602139.6	c.*2167T>C		3_prime_UTR_variant	9/9	5		P1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27470 AN: 152060 Hom.: 2676 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.188

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.181 AC: 27491 AN: 152178 Hom.: 2681 Cov.: 32 AF XY: 0.179 AC XY: 13314 AN XY: 74422

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.189

Alfa AF: 0.191 Hom.: 706

Bravo AF: 0.183

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12611411; hg19: chr19-50478932;