rs1327235

Variant names:

• chr20-10988382-A-G
• rs1327235
• ENST00000603180.5:n.220+209A>G

Variant summary

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

The ENST00000605292.5(ENSG00000270792):​n.440-3216A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,944 control chromosomes in the GnomAD database, including 16,408 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 (16408 hom., cov: 32)
• Consequence: ENSG00000270792 ENST00000605292.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

Genes affected

ENSG00000270792 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270792	ENST00000603180.5	n.220+209A>G		intron_variant	Intron 3 of 3	4
ENSG00000270792	ENST00000603985.1	n.83+1625A>G		intron_variant	Intron 1 of 2	4
ENSG00000270792	ENST00000605292.5	n.440-3216A>G		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69991 AN: 151826 Hom.: 16395 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.461 AC: 70038 AN: 151944 Hom.: 16408 Cov.: 32 AF XY: 0.457 AC XY: 33918 AN XY: 74272

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.546

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.451

Alfa AF: 0.460 Hom.: 17399

Bravo AF: 0.452

Asia WGS AF: 0.500 AC: 1737 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.062
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1327235; hg19: chr20-10969030;