rs199774

Variant names:

• chr20-22404679-G-A
• rs199774
• ENST00000377121.1:n.768+1950C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000377121.1(ENSG00000204684):​n.768+1950C>T variant causes a intron 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: ENSG00000204684 ENST00000377121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 4 publications found

Genes affected

ENSG00000204684 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC284788	NR_027089.2	n.768+1950C>T		intron_variant	Intron 2 of 3
LOC284788	NR_027090.1	n.685-3217C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204684	ENST00000377121.1	n.768+1950C>T		intron_variant	Intron 2 of 3	1
ENSG00000204684	ENST00000634280.1	n.353+1950C>T		intron_variant	Intron 3 of 4	5
ENSG00000204684	ENST00000635130.1	n.688+15281C>T		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.597 AC: 24780 AN: 41480

American (AMR) AF: 0.338 AC: 5169 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3608 AN: 5150

South Asian (SAS) AF: 0.398 AC: 1920 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1373 AN: 10602

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11279 AN: 67988

Other (OTH) AF: 0.306 AC: 647 AN: 2114

Alfa AF: 0.228 Hom.: 6633

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs199774; hg19: chr20-22385317;