1-53405413-G-C

Position:

• chr1-53405413-G-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BS1 BS2

The variant allele was found at a frequency of 0.0104 in 152,286 control chromosomes in the GnomAD database, including 9 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 0.010 (9 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0104 (1579/152286) while in subpopulation SAS AF= 0.0201 (97/4824). AF 95% confidence interval is 0.0169. There are 9 homozygotes in gnomad4. There are 766 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0104 AC: 1581 AN: 152168 Hom.: 9 Cov.: 33

Gnomad AFR AF: 0.00290

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0117

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0203

Gnomad FIN AF: 0.00830

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0101

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

GnomAD4 genome AF: 0.0104 AC: 1579 AN: 152286 Hom.: 9 Cov.: 33 AF XY: 0.0103 AC XY: 766 AN XY: 74462

Gnomad4 AFR AF: 0.00289

Gnomad4 AMR AF: 0.0117

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0201

Gnomad4 FIN AF: 0.00830

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.00995

Alfa AF: 0.00237 Hom.: 0

Bravo AF: 0.0106

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	22
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs114216682; hg19: chr1-53871085;