rs16989992

Positions:

• chr20-4673489-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000652447.1(ENSG00000293214):​n.87+11573A>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 0.0192 in 152,256 control chromosomes in the GnomAD database, including 35 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 0.019 (35 hom., cov: 32)
• Consequence: ENST00000652447.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0192 (2929/152256) while in subpopulation SAS AF= 0.0305 (147/4820). AF 95% confidence interval is 0.0265. There are 35 homozygotes in gnomad4. There are 1446 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 35 gene

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.87+11573A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0193 AC: 2931 AN: 152138 Hom.: 35 Cov.: 32

Gnomad AFR AF: 0.00442

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0134

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

GnomAD4 genome AF: 0.0192 AC: 2929 AN: 152256 Hom.: 35 Cov.: 32 AF XY: 0.0194 AC XY: 1446 AN XY: 74442

Gnomad4 AFR AF: 0.00440

Gnomad4 AMR AF: 0.0111

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.0133

Alfa AF: 0.0239 Hom.: 6

Bravo AF: 0.0160

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16989992; hg19: chr20-4654135;