rs1327235

Positions:

• chr20-10988382-A-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, non coding transcript 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: ENST00000605292.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000605292.5	n.440-3216A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000603180.5	n.220+209A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000603985.1	n.83+1625A>G		intron_variant, non_coding_transcript_variant		4

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;