1-73886165-C-T

Position:

• chr1-73886165-C-T

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 0.129 in 152,020 control chromosomes in the GnomAD database, including 1,313 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 0.13 (1313 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.73886165C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285778	ENST00000649962.1	n.271+19764G>A		intron_variant
ENSG00000285778	ENST00000667324.1	n.148+28964G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19649 AN: 151904 Hom.: 1313 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0996

Gnomad ASJ AF: 0.0871

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.129 AC: 19654 AN: 152020 Hom.: 1313 Cov.: 32 AF XY: 0.129 AC XY: 9576 AN XY: 74310

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0994

Gnomad4 ASJ AF: 0.0871

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.196

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.123

Alfa AF: 0.115 Hom.: 571

Bravo AF: 0.127

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.024
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6701710; hg19: chr1-74351848;