rs6545535

Positions:

• chr2-55987381-A-G
• chr2-55987381-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000606639.1(ENSG00000272180):​n.82+35142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,056 control chromosomes in the GnomAD database, including 12,758 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 0.37 (12758 hom., cov: 33)
• Consequence: ENSG00000272180 ENST00000606639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

Genes affected

ENSG00000272180 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR217HG	NR_126406.1	n.209-23499T>C		intron_variant
LOC105374690	XR_940109.3	n.587+35142A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000272180	ENST00000606639.1	n.82+35142A>G		intron_variant		1
MIR217HG	ENST00000446139.1	n.209-23499T>C		intron_variant		5
MIR217HG	ENST00000701602.1	n.407+6492T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56076 AN: 151938 Hom.: 12732 Cov.: 33

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0631

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.369 AC: 56162 AN: 152056 Hom.: 12758 Cov.: 33 AF XY: 0.362 AC XY: 26918 AN XY: 74336

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.342

Alfa AF: 0.289 Hom.: 12761

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6545535; hg19: chr2-56214516;