rs1930961

Positions:

• chr22-25479298-T-C

Variant summary

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

The XR_007068036.1(LOC124905094):​n.5142T>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 151,846 control chromosomes in the GnomAD database, including 7,425 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 (7425 hom., cov: 32)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: LOC124905094 XR_007068036.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

CRYBB2P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905094	XR_007068036.1	n.5142T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRYBB2P1	ENST00000354451.6	n.366+19783T>C		intron_variant		1
ENSG00000272977	ENST00000609475.1	n.3081T>C		non_coding_transcript_exon_variant	1/1	6
CRYBB2P1	ENST00000509460.4	n.568+19783T>C		intron_variant		3
CRYBB2P1	ENST00000686640.2	n.573+19783T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33986 AN: 151694 Hom.: 7383 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.0924

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.147 AC: 5 AN: 34 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 2 AN XY: 20

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.0909

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.225 AC: 34097 AN: 151812 Hom.: 7425 Cov.: 32 AF XY: 0.222 AC XY: 16466 AN XY: 74220

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.0701

Gnomad4 EAS AF: 0.0926

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0663

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.196

Alfa AF: 0.133 Hom.: 1297

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	-0.90
CADD	Benign	0.36
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1930961; hg19: chr22-25875265;