6-106373553-G-T

Variant names:

• chr6-106373553-G-T
• rs2787520
• NM_001371242.2:c.173+12472G>T

Variant summary

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

The NM_001371242.2(CRYBG1):​c.173+12472G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,008 control chromosomes in the GnomAD database, including 24,387 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 0.55 (24387 hom., cov: 32)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 4 publications found

Genes affected

CRYBG1 (HGNC:356): (crystallin beta-gamma domain containing 1) Predicted to enable carbohydrate binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001371242.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBG1	NM_001371242.2	MANE Select	c.173+12472G>T		intron	N/A	NP_001358171.1	Q9Y4K1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBG1	ENST00000633556.3	TSL:5 MANE Select	c.173+12472G>T		intron	N/A	ENSP00000488010.2	Q9Y4K1-3

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83403 AN: 151890 Hom.: 24404 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.549 AC: 83403 AN: 152008 Hom.: 24387 Cov.: 32 AF XY: 0.550 AC XY: 40878 AN XY: 74282

African (AFR) AF: 0.327 AC: 13535 AN: 41444

American (AMR) AF: 0.612 AC: 9341 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3764 AN: 5186

South Asian (SAS) AF: 0.606 AC: 2913 AN: 4810

European-Finnish (FIN) AF: 0.625 AC: 6600 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42967 AN: 67956

Other (OTH) AF: 0.583 AC: 1231 AN: 2112

Alfa AF: 0.610 Hom.: 33171

Bravo AF: 0.542

Asia WGS AF: 0.609 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.71
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs2787520; hg19: chr6-106821428; COSMIC: COSV69419448;