chr6-106419953-G-A

Variant names:

• chr6-106419953-G-A
• rs10485149
• NM_001371242.2:c.174-31741G>A

Variant summary

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

The NM_001371242.2(CRYBG1):​c.174-31741G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,222 control chromosomes in the GnomAD database, including 1,122 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 0.12 (1122 hom., cov: 32)
• Consequence: CRYBG1 NM_001371242.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRYBG1	NM_001371242.2	c.174-31741G>A		intron_variant	Intron 1 of 21	ENST00000633556.3	NP_001358171.1
CRYBG1	XM_047418270.1	c.251+21715G>A		intron_variant	Intron 2 of 22		XP_047274226.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRYBG1	ENST00000633556.3	c.174-31741G>A		intron_variant	Intron 1 of 21	5	NM_001371242.2	ENSP00000488010.2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17799 AN: 152104 Hom.: 1119 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.117 AC: 17830 AN: 152222 Hom.: 1122 Cov.: 32 AF XY: 0.112 AC XY: 8351 AN XY: 74424

African (AFR) AF: 0.149 AC: 6203 AN: 41536

American (AMR) AF: 0.112 AC: 1706 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.148 AC: 768 AN: 5184

South Asian (SAS) AF: 0.0580 AC: 280 AN: 4826

European-Finnish (FIN) AF: 0.0698 AC: 739 AN: 10592

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7308 AN: 68012

Other (OTH) AF: 0.109 AC: 229 AN: 2110

Alfa AF: 0.114 Hom.: 365

Bravo AF: 0.124

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.23
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10485149; hg19: chr6-106867828;