rs5761618

Positions:

• chr22-26597742-T-G

Variant summary

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

The ENST00000668614.1(ENSG00000286326):​n.56+659T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,982 control chromosomes in the GnomAD database, including 16,463 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 0.46 (16463 hom., cov: 32)
• Consequence: ENST00000668614.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.315

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CRYBA4	XM_006724140.4	c.-239+659T>G		intron_variant			XP_006724203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000668614.1	n.56+659T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69596 AN: 151864 Hom.: 16434 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69669 AN: 151982 Hom.: 16463 Cov.: 32 AF XY: 0.461 AC XY: 34230 AN XY: 74256

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.454

Alfa AF: 0.403 Hom.: 9476

Bravo AF: 0.458

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5761618; hg19: chr22-26993706;