rs199774

Positions:

• chr20-22404679-G-A

Variant summary

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

The NR_027090.1(LOC284788):​n.685-3217C>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 0.326 in 152,122 control chromosomes in the GnomAD database, including 11,275 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 0.33 (11275 hom., cov: 33)
• Consequence: LOC284788 NR_027090.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC284788	NR_027090.1	n.685-3217C>T		intron_variant, non_coding_transcript_variant
LOC284788	NR_027089.2	n.768+1950C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634280.1	n.353+1950C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49544 AN: 152004 Hom.: 11234 Cov.: 33

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.326 AC: 49639 AN: 152122 Hom.: 11275 Cov.: 33 AF XY: 0.327 AC XY: 24315 AN XY: 74382

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.306

Alfa AF: 0.210 Hom.: 4075

Bravo AF: 0.354

Asia WGS AF: 0.507 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199774; hg19: chr20-22385317;