chr1-53343358-T-C

Position:

• chr1-53343358-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 0.357 in 151,984 control chromosomes in the GnomAD database, including 10,285 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 0.36 (10285 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.795

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.53343358T>C		intergenic_region
LOC105378731	XR_001738057.2	n.73-373A>G		intron_variant
LOC105378731	XR_007066092.1	n.73-373A>G		intron_variant
LOC105378731	XR_007066093.1	n.73-373A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54259 AN: 151866 Hom.: 10278 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.357 AC: 54294 AN: 151984 Hom.: 10285 Cov.: 32 AF XY: 0.355 AC XY: 26372 AN XY: 74286

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.329

Alfa AF: 0.317 Hom.: 3495

Bravo AF: 0.364

Asia WGS AF: 0.382 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2782497; hg19: chr1-53809030;