1-78759941-C-T

Variant names:

• chr1-78759941-C-T
• rs1937023

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 0.134 in 152,058 control chromosomes in the GnomAD database, including 1,393 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 (1393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20297 AN: 151940 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.134 AC: 20309 AN: 152058 Hom.: 1393 Cov.: 32 AF XY: 0.132 AC XY: 9779 AN XY: 74312

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0998

Gnomad4 EAS AF: 0.0167

Gnomad4 SAS AF: 0.0875

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.107

Alfa AF: 0.130 Hom.: 674

Bravo AF: 0.131

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	21
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1937023; hg19: chr1-79225626;