rs6052761

Positions:

• chr20-4676371-T-C
• chr20-4676371-T-G

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.87+8691A>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 0.176 in 152,206 control chromosomes in the GnomAD database, including 3,086 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 0.18 (3086 hom., cov: 32)
• Consequence: ENST00000652447.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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
	ENST00000652447.1	n.87+8691A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26684 AN: 152088 Hom.: 3078 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0358

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.176 AC: 26717 AN: 152206 Hom.: 3086 Cov.: 32 AF XY: 0.178 AC XY: 13212 AN XY: 74414

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0357

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.145

Alfa AF: 0.112 Hom.: 1522

Bravo AF: 0.181

Asia WGS AF: 0.107 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.75
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6052761; hg19: chr20-4657017;