1-203238392-T-C

Position:

• chr1-203238392-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.887 in 152,170 control chromosomes in the GnomAD database, including 60,258 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 0.89 (60258 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.203238392T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHIT1	ENST00000484834.5	n.4382+2071A>G		intron_variant		2
CHIT1	ENST00000513472.5	n.151+2071A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134932 AN: 152052 Hom.: 60216 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.891

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

GnomAD4 genome AF: 0.887 AC: 135026 AN: 152170 Hom.: 60258 Cov.: 31 AF XY: 0.885 AC XY: 65866 AN XY: 74384

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.894

Alfa AF: 0.882 Hom.: 131035

Bravo AF: 0.873

Asia WGS AF: 0.801 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2494287; hg19: chr1-203207520;