rs1028555

Positions:

• chr20-5356895-T-C

Variant summary

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

The ENST00000668553.1(ENSG00000266908):​n.1120+35723T>C 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 0.429 in 152,034 control chromosomes in the GnomAD database, including 14,051 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 0.43 (14051 hom., cov: 32)
• Consequence: ENST00000668553.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 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
	ENST00000668553.1	n.1120+35723T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65142 AN: 151916 Hom.: 14032 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.429 AC: 65209 AN: 152034 Hom.: 14051 Cov.: 32 AF XY: 0.428 AC XY: 31817 AN XY: 74332

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.456

Alfa AF: 0.445 Hom.: 8316

Bravo AF: 0.432

Asia WGS AF: 0.479 AC: 1666 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1028555; hg19: chr20-5337541;