chr1-85615770-T-C

Position:

• chr1-85615770-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.227 in 152,162 control chromosomes in the GnomAD database, including 4,291 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 0.23 (4291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.41

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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: 0.227 AC: 34507 AN: 152044 Hom.: 4284 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.227 AC: 34539 AN: 152162 Hom.: 4291 Cov.: 32 AF XY: 0.226 AC XY: 16789 AN XY: 74380

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.256

Alfa AF: 0.258 Hom.: 8657

Bravo AF: 0.226

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	19
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12061951; hg19: chr1-86081453;