rs5994451

chr22-31927525-T-G

Variant summary

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

The XR_007068064.1(LOC124905102):n.165T>G variant causes a non coding transcript exon 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: LOC124905102 XR_007068064.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

LOC124905102 (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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905102	XR_007068064.1	n.165T>G		non_coding_transcript_exon_variant	2/2
LOC105372998	XR_001755494.2	n.1932-215A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
YWHAH-AS1	ENST00000484682.2	n.1461+638A>C		intron_variant, non_coding_transcript_variant		4
YWHAH-AS1	ENST00000641789.2	n.2289-234A>C		intron_variant, non_coding_transcript_variant
YWHAH-AS1	ENST00000654264.1	n.246-215A>C		intron_variant, non_coding_transcript_variant
YWHAH-AS1	ENST00000676309.1	n.200-215A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.394

Alfa AF: 0.334 Hom.: 15192

Bravo AF: 0.423

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5994451; hg19: chr22-32323511;