rs28386840

Variant names:

• chr16-55652906-T-A
• rs28386840
• XR_007065075.1:n.*200A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-55652906-T-A
• chr16-55652906-T-C
• chr16-55652906-T-G

Variant summary

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

The XR_007065075.1(LOC124903693):​n.*200A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 145,034 control chromosomes in the GnomAD database, including 29,748 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 0.64 (29748 hom., cov: 32)
• Consequence: LOC124903693 XR_007065075.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 50 publications found

Genes affected

LOC124903693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903693	XR_007065075.1	n.*200A>T		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.639 AC: 92600 AN: 144926 Hom.: 29725 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.639 AC: 92666 AN: 145034 Hom.: 29748 Cov.: 32 AF XY: 0.644 AC XY: 45735 AN XY: 70978

African (AFR) AF: 0.455 AC: 16248 AN: 35728

American (AMR) AF: 0.694 AC: 10456 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2258 AN: 3378

East Asian (EAS) AF: 0.559 AC: 2881 AN: 5156

South Asian (SAS) AF: 0.712 AC: 3414 AN: 4792

European-Finnish (FIN) AF: 0.735 AC: 7767 AN: 10564

Middle Eastern (MID) AF: 0.588 AC: 167 AN: 284

European-Non Finnish (NFE) AF: 0.709 AC: 47554 AN: 67106

Other (OTH) AF: 0.644 AC: 1319 AN: 2048

Alfa AF: 0.367 Hom.: 530

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.57
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs28386840; hg19: chr16-55686818;