chr22-25478613-A-C

Variant names:

• chr22-25478613-A-C
• rs7285549
• ENST00000354451.6:n.366+19098A>C

Variant summary

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

The ENST00000354451.6(CRYBB2P1):​n.366+19098A>C variant causes a intron 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: CRYBB2P1 ENST00000354451.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 11 publications found

Genes affected

CRYBB2P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124905094	XR_007068036.1	n.4457A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRYBB2P1	ENST00000354451.6	n.366+19098A>C		intron_variant	Intron 3 of 5	1
ENSG00000272977	ENST00000609475.1	n.2396A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
CRYBB2P1	ENST00000509460.5	n.573+19098A>C		intron_variant	Intron 4 of 5	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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 12

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.568 AC: 23506 AN: 41350

American (AMR) AF: 0.176 AC: 2680 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3468

East Asian (EAS) AF: 0.0923 AC: 478 AN: 5180

South Asian (SAS) AF: 0.161 AC: 772 AN: 4802

European-Finnish (FIN) AF: 0.0665 AC: 705 AN: 10598

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.0777 AC: 5278 AN: 67968

Other (OTH) AF: 0.196 AC: 415 AN: 2112

Alfa AF: 0.121 Hom.: 1121

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7285549; hg19: chr22-25874580;