1-208545397-C-T

Position:

• chr1-208545397-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0184 in 152,178 control chromosomes in the GnomAD database, including 36 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 0.018 (36 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0184 (2797/152178) while in subpopulation AFR AF= 0.0309 (1281/41516). AF 95% confidence interval is 0.0295. There are 36 homozygotes in gnomad4. There are 1255 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 36 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.208545397C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2797 AN: 152060 Hom.: 36 Cov.: 31

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0184 AC: 2797 AN: 152178 Hom.: 36 Cov.: 31 AF XY: 0.0169 AC XY: 1255 AN XY: 74404

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.0191

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0214

Gnomad4 FIN AF: 0.000189

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0154 Hom.: 10

Bravo AF: 0.0209

Asia WGS AF: 0.0120 AC: 42 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	0.012
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494900; hg19: chr1-208718742;