ENST00000354451.6:n.366+19098A>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000354451.6. 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
	CRYBB2P1	ENST00000354451.6	TSL:1	n.366+19098A>C		intron	N/A
	ENSG00000272977	ENST00000609475.1	TSL:6	n.2396A>C		non_coding_transcript_exon	Exon 1 of 1
	CRYBB2P1	ENST00000509460.5	TSL:3	n.573+19098A>C		intron	N/A

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 v4.9

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;