rs16844374

chr2-159829591-T-C

Variant summary

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

The NM_002349.4(LY75):c.3958+2079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,154 control chromosomes in the GnomAD database, including 2,293 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 0.16 (2293 hom., cov: 33)
• Consequence: LY75 NM_002349.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

Genes affected

LY75 (HGNC:6729): (lymphocyte antigen 75) Predicted to enable signaling receptor activity. Predicted to be involved in immune response and inflammatory response. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

LY75-CD302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY75	NM_002349.4	c.3958+2079A>G		intron_variant		ENST00000263636.5
LY75-CD302	NM_001198760.1	c.3958+2079A>G		intron_variant
LY75-CD302	NM_001198759.1	c.3958+2079A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY75	ENST00000263636.5	c.3958+2079A>G		intron_variant		1	NM_002349.4	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24539 AN: 152036 Hom.: 2289 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.161 AC: 24568 AN: 152154 Hom.: 2293 Cov.: 33 AF XY: 0.164 AC XY: 12205 AN XY: 74390

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.177

Alfa AF: 0.161 Hom.: 269

Bravo AF: 0.176

Asia WGS AF: 0.243 AC: 842 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.58

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs16844374; hg19: chr2-160686102;