1-203215760-T-C

Position:

• chr1-203215760-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 0.492 in 151,976 control chromosomes in the GnomAD database, including 19,494 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 0.49 (19494 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.203215760T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHIT1	ENST00000479483.1	n.283+1979A>G		intron_variant		3
CHIT1	ENST00000484834.5	n.5388+1979A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74703 AN: 151858 Hom.: 19474 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.492 AC: 74766 AN: 151976 Hom.: 19494 Cov.: 32 AF XY: 0.503 AC XY: 37355 AN XY: 74276

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.521

Alfa AF: 0.467 Hom.: 4762

Bravo AF: 0.494

Asia WGS AF: 0.807 AC: 2801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417149; hg19: chr1-203184888;