rs27807

Variant names:

• chr16-49404129-A-G
• rs27807
• ENST00000849660.1:n.585+5220T>C

Variant summary

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

The ENST00000849660.1(ENSG00000262950):​n.585+5220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,742 control chromosomes in the GnomAD database, including 18,498 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 0.46 (18498 hom., cov: 30)
• Consequence: ENSG00000262950 ENST00000849660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 4 publications found

Genes affected

ENSG00000262950 (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 = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371244	XR_001752167.2	n.1812+5220T>C		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262950	ENST00000849660.1	n.585+5220T>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69234 AN: 151622 Hom.: 18468 Cov.: 30

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.457 AC: 69312 AN: 151742 Hom.: 18498 Cov.: 30 AF XY: 0.452 AC XY: 33479 AN XY: 74116

African (AFR) AF: 0.746 AC: 30858 AN: 41342

American (AMR) AF: 0.281 AC: 4289 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1488 AN: 3464

East Asian (EAS) AF: 0.378 AC: 1941 AN: 5130

South Asian (SAS) AF: 0.504 AC: 2415 AN: 4794

European-Finnish (FIN) AF: 0.315 AC: 3313 AN: 10518

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23594 AN: 67928

Other (OTH) AF: 0.421 AC: 890 AN: 2112

Alfa AF: 0.382 Hom.: 6811

Bravo AF: 0.462

Asia WGS AF: 0.472 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs27807; hg19: chr16-49438040;