rs11699291

Positions:

• chr20-48268200-G-A

Variant summary

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

The ENST00000668815.1(ENSG00000288083):​n.116-2675C>T 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 0.0455 in 152,258 control chromosomes in the GnomAD database, including 201 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 0.045 (201 hom., cov: 33)
• Consequence: ENST00000668815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0455 (6922/152258) while in subpopulation EAS AF= 0.0526 (273/5186). AF 95% confidence interval is 0.0477. There are 201 homozygotes in gnomad4. There are 3361 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 201 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668815.1	n.116-2675C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0455 AC: 6916 AN: 152142 Hom.: 201 Cov.: 33

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.0389

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0491

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0455 AC: 6922 AN: 152258 Hom.: 201 Cov.: 33 AF XY: 0.0452 AC XY: 3361 AN XY: 74436

Gnomad4 AFR AF: 0.0438

Gnomad4 AMR AF: 0.0384

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0526

Gnomad4 SAS AF: 0.0459

Gnomad4 FIN AF: 0.0389

Gnomad4 NFE AF: 0.0491

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0449 Hom.: 26

Bravo AF: 0.0454

Asia WGS AF: 0.0490 AC: 171 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11699291; hg19: chr20-46896943;