rs5994451

Variant names:

• chr22-31927525-T-G
• rs5994451
• ENST00000646701.1:c.1787-28614T>G

Variant summary

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

The ENST00000646701.1(ENSG00000285404):​c.1787-28614T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,984 control chromosomes in the GnomAD database, including 13,859 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 0.41 (13859 hom., cov: 32)
• Consequence: ENSG00000285404 ENST00000646701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 6 publications found

Genes affected

ENSG00000285404 (HGNC:):

YWHAH-AS1 (HGNC:23051): (YWHAH antisense RNA 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646701.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285404	ENST00000646701.1		c.1787-28614T>G		intron	N/A	ENSP00000496158.1
	ENSG00000306617	ENST00000819773.1		n.231T>G		non_coding_transcript_exon	Exon 2 of 2
	YWHAH-AS1	ENST00000484682.2	TSL:4	n.1461+638A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62315 AN: 151864 Hom.: 13803 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.411 AC: 62423 AN: 151984 Hom.: 13859 Cov.: 32 AF XY: 0.415 AC XY: 30867 AN XY: 74290

African (AFR) AF: 0.562 AC: 23268 AN: 41420

American (AMR) AF: 0.486 AC: 7420 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3468

East Asian (EAS) AF: 0.281 AC: 1456 AN: 5174

South Asian (SAS) AF: 0.424 AC: 2042 AN: 4814

European-Finnish (FIN) AF: 0.421 AC: 4450 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21600 AN: 67968

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.346 Hom.: 38656

Bravo AF: 0.423

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs5994451; hg19: chr22-32323511;