6-106373342-G-C

Variant names:

• chr6-106373342-G-C
• rs553307
• NM_001371242.2:c.173+12261G>C

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+12261G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 152,130 control chromosomes in the GnomAD database, including 56,429 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 0.86 (56429 hom., cov: 31)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.913 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBG1	NM_001371242.2	MANE Select	c.173+12261G>C		intron	N/A	NP_001358171.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBG1	ENST00000633556.3	TSL:5 MANE Select	c.173+12261G>C		intron	N/A	ENSP00000488010.2

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130201 AN: 152012 Hom.: 56422 Cov.: 31

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.919

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.856 AC: 130261 AN: 152130 Hom.: 56429 Cov.: 31 AF XY: 0.859 AC XY: 63911 AN XY: 74368

African (AFR) AF: 0.719 AC: 29777 AN: 41426

American (AMR) AF: 0.889 AC: 13594 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2937 AN: 3470

East Asian (EAS) AF: 0.818 AC: 4230 AN: 5172

South Asian (SAS) AF: 0.878 AC: 4235 AN: 4826

European-Finnish (FIN) AF: 0.947 AC: 10043 AN: 10600

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.919 AC: 62522 AN: 68028

Other (OTH) AF: 0.874 AC: 1840 AN: 2106

Alfa AF: 0.877 Hom.: 2955

Bravo AF: 0.845

Asia WGS AF: 0.834 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs553307; hg19: chr6-106821217; COSMIC: COSV50466092;