rs7285549

Positions:

• chr22-25478613-A-C

Variant summary

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

The ENST00000609475.1(ENSG00000272977):​n.2396A>C 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 0.225 in 151,954 control chromosomes in the GnomAD database, including 7,438 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 0.22 (7438 hom., cov: 33)
  • Exomes 𝑓: 0.071 (0 hom.)
• Consequence: ENST00000609475.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

(HGNC:):

CRYBB2P1 (HGNC:2399): (crystallin beta B2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905094	XR_007068036.1	n.4457A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000609475.1	n.2396A>C		non_coding_transcript_exon_variant	1/1
CRYBB2P1	ENST00000354451.6	n.366+19098A>C		intron_variant, non_coding_transcript_variant		1
CRYBB2P1	ENST00000686640.2	n.573+19098A>C		intron_variant, non_coding_transcript_variant
CRYBB2P1	ENST00000509460.4	n.568+19098A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.224 AC: 34027 AN: 151822 Hom.: 7396 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.0921

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.0714 AC: 1 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.225 AC: 34138 AN: 151940 Hom.: 7438 Cov.: 33 AF XY: 0.222 AC XY: 16497 AN XY: 74286

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.196

Alfa AF: 0.125 Hom.: 1065

Bravo AF: 0.249

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7285549; hg19: chr22-25874580;