chr17-74608037-T-A

Variant names:

• chr17-74608037-T-A
• rs492256
• ENST00000838315.1:n.571+1411T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_158152.1(LOC101928343):​n.2503+1411T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,132 control chromosomes in the GnomAD database, including 28,822 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 0.59 (28822 hom., cov: 32)
• Consequence: LOC101928343 NR_158152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 publications found

Genes affected

CD300LD-AS1 (HGNC:26480): (CD300LD antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LOC101928343 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_158152.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101928343	NR_158152.1		n.2503+1411T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD300LD-AS1	ENST00000838315.1		n.571+1411T>A		intron	N/A
	CD300LD-AS1	ENST00000838318.1		n.480+1411T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90115 AN: 152014 Hom.: 28758 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.593 AC: 90241 AN: 152132 Hom.: 28822 Cov.: 32 AF XY: 0.589 AC XY: 43785 AN XY: 74362

African (AFR) AF: 0.848 AC: 35198 AN: 41526

American (AMR) AF: 0.451 AC: 6888 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1977 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1781 AN: 5174

South Asian (SAS) AF: 0.574 AC: 2766 AN: 4822

European-Finnish (FIN) AF: 0.517 AC: 5468 AN: 10576

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34298 AN: 67978

Other (OTH) AF: 0.584 AC: 1231 AN: 2108

Alfa AF: 0.391 Hom.: 966

Bravo AF: 0.598

Asia WGS AF: 0.489 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs492256; hg19: chr17-72604176;