rs166848

Variant names:

• chr2-199889178-T-C
• rs166848
• ENST00000417006.5:n.406+5405A>G

Variant summary

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

The ENST00000417006.5(ENSG00000232732):​n.406+5405A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,000 control chromosomes in the GnomAD database, including 52,383 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 0.83 (52383 hom., cov: 30)
• Consequence: ENSG00000232732 ENST00000417006.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 3 publications found

Genes affected

ENSG00000232732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927687	XR_923766.4	n.193-9568A>G		intron_variant	Intron 2 of 3
LOC101927687	XR_923769.4	n.193-6582A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232732	ENST00000417006.5	n.406+5405A>G		intron_variant	Intron 4 of 4	3
ENSG00000232732	ENST00000457577.7	n.351+19925A>G		intron_variant	Intron 2 of 2	3
ENSG00000232732	ENST00000593735.6	n.261-9568A>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.830 AC: 125990 AN: 151882 Hom.: 52327 Cov.: 30

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.830 AC: 126104 AN: 152000 Hom.: 52383 Cov.: 30 AF XY: 0.830 AC XY: 61638 AN XY: 74268

African (AFR) AF: 0.847 AC: 35101 AN: 41460

American (AMR) AF: 0.897 AC: 13705 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4101 AN: 5158

South Asian (SAS) AF: 0.908 AC: 4376 AN: 4822

European-Finnish (FIN) AF: 0.744 AC: 7853 AN: 10560

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55121 AN: 67940

Other (OTH) AF: 0.843 AC: 1783 AN: 2114

Alfa AF: 0.810 Hom.: 6194

Bravo AF: 0.840

Asia WGS AF: 0.855 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.39
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs166848; hg19: chr2-200753901;