1-86193766-T-A

Variant names:

• chr1-86193766-T-A
• rs1507274

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 0.16 in 152,170 control chromosomes in the GnomAD database, including 2,162 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 0.16 (2162 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.327 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: 0.160 AC: 24347 AN: 152052 Hom.: 2166 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.160 AC: 24343 AN: 152170 Hom.: 2162 Cov.: 32 AF XY: 0.159 AC XY: 11826 AN XY: 74414

African (AFR) AF: 0.198 AC: 8199 AN: 41496

American (AMR) AF: 0.117 AC: 1792 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3472

East Asian (EAS) AF: 0.341 AC: 1766 AN: 5184

South Asian (SAS) AF: 0.256 AC: 1235 AN: 4828

European-Finnish (FIN) AF: 0.0890 AC: 944 AN: 10602

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9360 AN: 68000

Other (OTH) AF: 0.175 AC: 369 AN: 2110

Alfa AF: 0.140 Hom.: 195

Bravo AF: 0.162

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.68
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs1507274; hg19: chr1-86659449;