rs27545

Variant names:

• chr5-68725382-C-A
• rs27545
• ENST00000507733.3:n.313+20071G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-68725382-C-A
• chr5-68725382-C-G

Variant summary

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

The ENST00000507733.3(ENSG00000248884):​n.313+20071G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,956 control chromosomes in the GnomAD database, including 9,971 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 0.36 (9971 hom., cov: 32)
• Consequence: ENSG00000248884 ENST00000507733.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 1 publications found

Genes affected

ENSG00000248884 (HGNC:58096):

LOC105379013 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507733.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248884	ENST00000507733.3	TSL:2	n.313+20071G>T		intron	N/A
	ENSG00000248884	ENST00000688207.1		n.65+34206G>T		intron	N/A
	ENSG00000248884	ENST00000717704.1		n.110+34206G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54078 AN: 151838 Hom.: 9972 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.356 AC: 54093 AN: 151956 Hom.: 9971 Cov.: 32 AF XY: 0.352 AC XY: 26156 AN XY: 74234

African (AFR) AF: 0.410 AC: 16979 AN: 41414

American (AMR) AF: 0.260 AC: 3978 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1185 AN: 3468

East Asian (EAS) AF: 0.115 AC: 596 AN: 5178

South Asian (SAS) AF: 0.397 AC: 1911 AN: 4812

European-Finnish (FIN) AF: 0.338 AC: 3555 AN: 10524

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24719 AN: 67970

Other (OTH) AF: 0.371 AC: 782 AN: 2108

Alfa AF: 0.343 Hom.: 12414

Bravo AF: 0.346

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs27545;

hg19: chr5-68021209;

COSMIC: COSV60152098;