1-55340792-T-C

Position:

• chr1-55340792-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 0.942 in 152,294 control chromosomes in the GnomAD database, including 67,693 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 0.94 (67693 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55340792T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000234810	ENST00000643167.1	n.138+11367T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.942 AC: 143348 AN: 152176 Hom.: 67636 Cov.: 33

Gnomad AFR AF: 0.986

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.942 AC: 143464 AN: 152294 Hom.: 67693 Cov.: 33 AF XY: 0.943 AC XY: 70211 AN XY: 74464

Gnomad4 AFR AF: 0.986

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.940

Alfa AF: 0.923 Hom.: 25456

Bravo AF: 0.947

Asia WGS AF: 0.983 AC: 3418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs207150; hg19: chr1-55806465;