1-119366891-A-G

Variant names:

• chr1-119366891-A-G
• rs3753264

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 0.463 in 152,090 control chromosomes in the GnomAD database, including 19,217 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 0.46 (19217 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.463 AC: 70389 AN: 151972 Hom.: 19175 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.463 AC: 70490 AN: 152090 Hom.: 19217 Cov.: 32 AF XY: 0.465 AC XY: 34570 AN XY: 74332

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.434

Alfa AF: 0.351 Hom.: 13443

Bravo AF: 0.474

Asia WGS AF: 0.560 AC: 1948 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753264; hg19: chr1-119909514;