1-78772330-T-C

Position:

• chr1-78772330-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 0.288 in 152,090 control chromosomes in the GnomAD database, including 6,648 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 0.29 (6648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

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: 0.288 AC: 43831 AN: 151972 Hom.: 6645 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.288 AC: 43849 AN: 152090 Hom.: 6648 Cov.: 32 AF XY: 0.287 AC XY: 21321 AN XY: 74364

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.0455

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.260

Alfa AF: 0.312 Hom.: 9344

Bravo AF: 0.281

Asia WGS AF: 0.159 AC: 555 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	7.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4650608; hg19: chr1-79238015;