rs1881345

Variant names:

• chr16-8398638-T-A
• rs1881345
• XR_933045.2:n.358-5016T>A

Variant summary

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

The XR_933045.2(LOC105371072):​n.358-5016T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0626 in 152,168 control chromosomes in the GnomAD database, including 316 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 0.063 (316 hom., cov: 32)
• Consequence: LOC105371072 XR_933045.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 1 publications found

Genes affected

LOC105371072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.072 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371072	XR_933045.2	n.358-5016T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9512 AN: 152050 Hom.: 315 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0541

Gnomad OTH AF: 0.0631

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

GnomAD4 genome AF: 0.0626 AC: 9523 AN: 152168 Hom.: 316 Cov.: 32 AF XY: 0.0631 AC XY: 4697 AN XY: 74388

African (AFR) AF: 0.0714 AC: 2965 AN: 41528

American (AMR) AF: 0.0741 AC: 1133 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3470

East Asian (EAS) AF: 0.0783 AC: 404 AN: 5162

South Asian (SAS) AF: 0.0590 AC: 284 AN: 4816

European-Finnish (FIN) AF: 0.0657 AC: 695 AN: 10582

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0541 AC: 3679 AN: 67998

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0584 Hom.: 42

Bravo AF: 0.0627

Asia WGS AF: 0.102 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.2
DANN	Benign	0.47
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1881345; hg19: chr16-8448640;