chr1-86222702-T-C

Position:

• chr1-86222702-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 0.928 in 152,288 control chromosomes in the GnomAD database, including 65,698 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 0.93 (65698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141245 AN: 152170 Hom.: 65645 Cov.: 32

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.928 AC: 141354 AN: 152288 Hom.: 65698 Cov.: 32 AF XY: 0.923 AC XY: 68725 AN XY: 74452

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.929

Alfa AF: 0.918 Hom.: 8818

Bravo AF: 0.936

Asia WGS AF: 0.888 AC: 3085 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1336049; hg19: chr1-86688385;