rs4802644

chr19-49974133-G-Achr19-49974133-G-T

Variant summary

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

The NR_145574.2(SIGLEC16):n.2126G>A 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 0.107 in 152,220 control chromosomes in the GnomAD database, including 1,131 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 0.11 (1131 hom., cov: 32)
• Consequence: SIGLEC16 NR_145574.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIGLEC16	NR_145574.2	n.2126G>A		non_coding_transcript_exon_variant	9/9
SIGLEC16	NM_001348364.2	c.*646G>A		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIGLEC16	ENST00000602139.6	c.*625G>A		3_prime_UTR_variant	9/9	5		P1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16217 AN: 152102 Hom.: 1129 Cov.: 32

Gnomad AFR AF: 0.0481

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.107 AC: 16223 AN: 152220 Hom.: 1131 Cov.: 32 AF XY: 0.107 AC XY: 7956 AN XY: 74408

Gnomad4 AFR AF: 0.0482

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.113

Alfa AF: 0.107 Hom.: 162

Bravo AF: 0.107

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.1
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4802644; hg19: chr19-50477390;