1-86222702-T-C

Variant names:

• chr1-86222702-T-C
• rs1336049

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.954 AC: 39664 AN: 41570

American (AMR) AF: 0.934 AC: 14290 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3362 AN: 3472

East Asian (EAS) AF: 0.968 AC: 5022 AN: 5188

South Asian (SAS) AF: 0.809 AC: 3893 AN: 4814

European-Finnish (FIN) AF: 0.880 AC: 9333 AN: 10610

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62785 AN: 68022

Other (OTH) AF: 0.929 AC: 1961 AN: 2112

Alfa AF: 0.919 Hom.: 18076

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1336049; hg19: chr1-86688385;