chr1-86222702-T-C

Variant names:

• chr1-86222702-T-C
• rs1336049

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;