6-106451351-C-T

Variant names:

• chr6-106451351-C-T
• rs1417352
• NM_001371242.2:c.174-343C>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.174-343C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 165,756 control chromosomes in the GnomAD database, including 41,474 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 0.71 (37943 hom., cov: 32)
  • Exomes 𝑓: 0.72 (3531 hom.)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 14 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]

ENSG00000282408 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 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.174-343C>T		intron	N/A	NP_001358171.1	Q9Y4K1-3
	LOC105377924	NR_134603.1		n.*145G>A		downstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRYBG1	ENST00000633556.3	TSL:5 MANE Select	c.174-343C>T		intron	N/A	ENSP00000488010.2	Q9Y4K1-3
	ENSG00000282408	ENST00000632749.2	TSL:2	n.*145G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107224 AN: 151920 Hom.: 37893 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.719

GnomAD4 exome AF: 0.715 AC: 9814 AN: 13718 Hom.: 3531 AF XY: 0.717 AC XY: 5029 AN XY: 7014

African (AFR) AF: 0.702 AC: 369 AN: 526

American (AMR) AF: 0.733 AC: 305 AN: 416

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 562 AN: 672

East Asian (EAS) AF: 0.651 AC: 617 AN: 948

South Asian (SAS) AF: 0.643 AC: 287 AN: 446

European-Finnish (FIN) AF: 0.655 AC: 296 AN: 452

Middle Eastern (MID) AF: 0.815 AC: 75 AN: 92

European-Non Finnish (NFE) AF: 0.719 AC: 6603 AN: 9188

Other (OTH) AF: 0.716 AC: 700 AN: 978

GnomAD4 genome AF: 0.706 AC: 107329 AN: 152038 Hom.: 37943 Cov.: 32 AF XY: 0.705 AC XY: 52386 AN XY: 74310

African (AFR) AF: 0.707 AC: 29288 AN: 41450

American (AMR) AF: 0.709 AC: 10829 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2846 AN: 3472

East Asian (EAS) AF: 0.658 AC: 3398 AN: 5164

South Asian (SAS) AF: 0.638 AC: 3078 AN: 4822

European-Finnish (FIN) AF: 0.646 AC: 6817 AN: 10554

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48587 AN: 67974

Other (OTH) AF: 0.722 AC: 1524 AN: 2112

Alfa AF: 0.715 Hom.: 161831

Bravo AF: 0.713

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.62
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs1417352; hg19: chr6-106899226;