rs6037908

chr20-4636745-A-G

Variant summary

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

The ENST00000652447.1(ENSG00000293214):n.88-6524T>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 0.215 in 152,036 control chromosomes in the GnomAD database, including 3,623 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 0.22 (3623 hom., cov: 31)
• Consequence: ENST00000652447.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225

Genes affected

(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 (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652447.1	n.88-6524T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32703 AN: 151918 Hom.: 3617 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0521

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.215 AC: 32730 AN: 152036 Hom.: 3623 Cov.: 31 AF XY: 0.211 AC XY: 15716 AN XY: 74316

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0523

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.188

Alfa AF: 0.223 Hom.: 5143

Bravo AF: 0.208

Asia WGS AF: 0.142 AC: 492 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.2
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6037908; hg19: chr20-4617391;